Starting phenix.real_space_refine on Thu Jul 24 17:44:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fdk_31546/07_2025/7fdk_31546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdk_31546/07_2025/7fdk_31546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fdk_31546/07_2025/7fdk_31546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdk_31546/07_2025/7fdk_31546.map" model { file = "/net/cci-nas-00/data/ceres_data/7fdk_31546/07_2025/7fdk_31546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdk_31546/07_2025/7fdk_31546.cif" } resolution = 3.69 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4113 2.51 5 N 1076 2.21 5 O 1223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6449 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4860 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 26, 'TRANS': 570} Conformer: "B" Number of residues, atoms: 597, 4860 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 26, 'TRANS': 570} bond proxies already assigned to first conformer: 4986 Chain: "E" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1540 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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 Time building chain proxies: 5.90, per 1000 atoms: 0.91 Number of scatterers: 6449 At special positions: 0 Unit cell: (118.56, 83.2, 80.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1223 8.00 N 1076 7.00 C 4113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 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 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 53 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 1.4 seconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 50.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.883A pdb=" N ASN A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 79 removed outlier: 4.058A pdb=" N SER A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.614A pdb=" N THR A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 Proline residue: A 178 - end of helix removed outlier: 3.962A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 231 removed outlier: 4.171A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.540A pdb=" N LYS A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.561A pdb=" N THR A 282 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.526A pdb=" N ALA A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.808A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.248A pdb=" N ALA A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 removed outlier: 4.328A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.432A 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 465 removed outlier: 4.036A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.549A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.439A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 4.528A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.529A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 383 through 390 Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.638A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.524A pdb=" N ASP E 442 " --> pdb=" O SER E 438 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.405A 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 352 removed outlier: 6.426A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 355 removed outlier: 4.005A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 270 hydrogen bonds defined for protein. 788 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: 1.49 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2071 1.34 - 1.46: 1721 1.46 - 1.58: 2781 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6631 Sorted by residual: bond pdb=" C LYS A 359 " pdb=" N MET A 360 " ideal model delta sigma weight residual 1.330 1.535 -0.205 1.23e-02 6.61e+03 2.79e+02 bond pdb=" C ILE A 358 " pdb=" N LYS A 359 " ideal model delta sigma weight residual 1.331 1.551 -0.221 1.66e-02 3.63e+03 1.77e+02 bond pdb=" C ALA E 397 " pdb=" N ASP E 398 " ideal model delta sigma weight residual 1.328 1.432 -0.104 1.42e-02 4.96e+03 5.37e+01 bond pdb=" C ASP E 398 " pdb=" N SER E 399 " ideal model delta sigma weight residual 1.332 1.392 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" C SER A 563 " pdb=" N GLU A 564 " ideal model delta sigma weight residual 1.335 1.231 0.104 3.04e-02 1.08e+03 1.16e+01 ... (remaining 6626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 8756 2.24 - 4.47: 219 4.47 - 6.71: 29 6.71 - 8.95: 2 8.95 - 11.18: 4 Bond angle restraints: 9010 Sorted by residual: angle pdb=" O ILE A 358 " pdb=" C ILE A 358 " pdb=" N LYS A 359 " ideal model delta sigma weight residual 123.26 134.44 -11.18 1.08e+00 8.57e-01 1.07e+02 angle pdb=" CA ILE A 358 " pdb=" C ILE A 358 " pdb=" N LYS A 359 " ideal model delta sigma weight residual 116.31 105.62 10.69 1.14e+00 7.69e-01 8.79e+01 angle pdb=" N GLN A 86 " pdb=" CA GLN A 86 " pdb=" C GLN A 86 " ideal model delta sigma weight residual 114.56 108.10 6.46 1.27e+00 6.20e-01 2.59e+01 angle pdb=" O ALA E 397 " pdb=" C ALA E 397 " pdb=" N ASP E 398 " ideal model delta sigma weight residual 123.27 129.19 -5.92 1.17e+00 7.31e-01 2.56e+01 angle pdb=" CA ALA E 397 " pdb=" C ALA E 397 " pdb=" N ASP E 398 " ideal model delta sigma weight residual 116.45 110.39 6.06 1.23e+00 6.61e-01 2.43e+01 ... (remaining 9005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 3478 17.73 - 35.45: 361 35.45 - 53.18: 74 53.18 - 70.91: 18 70.91 - 88.64: 10 Dihedral angle restraints: 3941 sinusoidal: 1615 harmonic: 2326 Sorted by residual: dihedral pdb=" CA GLU A 145 " pdb=" C GLU A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta harmonic sigma weight residual -180.00 -130.48 -49.52 0 5.00e+00 4.00e-02 9.81e+01 dihedral pdb=" CA VAL A 581 " pdb=" C VAL A 581 " pdb=" N LYS A 582 " pdb=" CA LYS A 582 " ideal model delta harmonic sigma weight residual 180.00 150.16 29.84 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA CYS E 361 " pdb=" C CYS E 361 " pdb=" N VAL E 362 " pdb=" CA VAL E 362 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 3938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 523 0.036 - 0.072: 311 0.072 - 0.108: 84 0.108 - 0.144: 22 0.144 - 0.180: 4 Chirality restraints: 944 Sorted by residual: chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA PRO E 337 " pdb=" N PRO E 337 " pdb=" C PRO E 337 " pdb=" CB PRO E 337 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA ILE E 434 " pdb=" N ILE E 434 " pdb=" C ILE E 434 " pdb=" CB ILE E 434 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 941 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO A 146 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 453 " 0.021 2.00e-02 2.50e+03 1.68e-02 5.68e+00 pdb=" CG TYR E 453 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR E 453 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 453 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 453 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 389 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " -0.031 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 138 2.64 - 3.21: 6520 3.21 - 3.77: 9963 3.77 - 4.34: 13424 4.34 - 4.90: 21531 Nonbonded interactions: 51576 Sorted by model distance: nonbonded pdb=" OH TYR A 41 " pdb=" O THR E 500 " model vdw 2.080 3.040 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.113 3.040 nonbonded pdb=" OH TYR A 535 " pdb=" O SER A 538 " model vdw 2.117 3.040 nonbonded pdb=" O ILE E 418 " pdb=" N ASP E 420 " model vdw 2.122 3.120 nonbonded pdb=" OH TYR A 535 " pdb=" O LYS A 541 " model vdw 2.156 3.040 ... (remaining 51571 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 group one per residue 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: 0.570 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.800 Find NCS groups from input model: 0.060 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.008 0.221 6637 Z= 0.439 Angle : 0.889 11.185 9025 Z= 0.523 Chirality : 0.048 0.180 944 Planarity : 0.006 0.069 1167 Dihedral : 15.522 88.637 2442 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.21 % Favored : 86.66 % Rotamer: Outliers : 0.29 % Allowed : 6.83 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -4.54 (0.24), residues: 788 helix: -2.30 (0.21), residues: 373 sheet: -3.02 (0.68), residues: 44 loop : -3.82 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 302 HIS 0.006 0.002 HIS A 378 PHE 0.028 0.003 PHE A 390 TYR 0.041 0.002 TYR E 453 ARG 0.003 0.000 ARG E 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00919 ( 3) link_NAG-ASN : angle 3.36865 ( 9) hydrogen bonds : bond 0.16363 ( 270) hydrogen bonds : angle 7.44417 ( 788) SS BOND : bond 0.00350 ( 3) SS BOND : angle 2.12552 ( 6) covalent geometry : bond 0.00848 ( 6631) covalent geometry : angle 0.88154 ( 9010) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 HIS cc_start: 0.8167 (p-80) cc_final: 0.7876 (p90) REVERT: A 297 MET cc_start: 0.6037 (ptt) cc_final: 0.5796 (ptp) REVERT: A 454 TYR cc_start: 0.7576 (t80) cc_final: 0.7248 (t80) REVERT: E 346 ARG cc_start: 0.7135 (ttm110) cc_final: 0.5726 (ptt180) REVERT: E 356 LYS cc_start: 0.8944 (tttm) cc_final: 0.8680 (ttmt) REVERT: E 357 ARG cc_start: 0.8591 (ttt90) cc_final: 0.6566 (mtt180) REVERT: E 424 LYS cc_start: 0.8907 (tptp) cc_final: 0.8506 (tttp) REVERT: E 451 TYR cc_start: 0.8044 (m-80) cc_final: 0.7096 (m-80) REVERT: E 462 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8407 (mtpp) REVERT: E 465 GLU cc_start: 0.6060 (tp30) cc_final: 0.5740 (tp30) REVERT: E 466 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8212 (ttm110) REVERT: E 467 ASP cc_start: 0.7996 (t0) cc_final: 0.7492 (t70) REVERT: E 508 TYR cc_start: 0.8344 (m-80) cc_final: 0.7998 (m-80) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.2377 time to fit residues: 29.8413 Evaluate side-chains 77 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 33 ASN A 34 GLN A 134 ASN A 195 ASN A 388 GLN A 522 GLN A 599 ASN E 460 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111690 restraints weight = 19853.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113934 restraints weight = 10495.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.114242 restraints weight = 9184.879| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6637 Z= 0.162 Angle : 0.681 8.228 9025 Z= 0.347 Chirality : 0.044 0.217 944 Planarity : 0.006 0.062 1167 Dihedral : 7.028 58.281 932 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.53 % Favored : 90.34 % Rotamer: Outliers : 1.45 % Allowed : 11.19 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.26 % 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: -2.92 (0.27), residues: 788 helix: -0.68 (0.25), residues: 370 sheet: -2.75 (0.64), residues: 50 loop : -3.23 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 163 HIS 0.004 0.001 HIS A 373 PHE 0.017 0.002 PHE A 390 TYR 0.016 0.002 TYR E 495 ARG 0.006 0.001 ARG E 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 3) link_NAG-ASN : angle 2.52121 ( 9) hydrogen bonds : bond 0.04865 ( 270) hydrogen bonds : angle 5.36414 ( 788) SS BOND : bond 0.00139 ( 3) SS BOND : angle 1.88268 ( 6) covalent geometry : bond 0.00374 ( 6631) covalent geometry : angle 0.67496 ( 9010) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6638 (mm-40) cc_final: 0.6171 (pp30) REVERT: A 152 MET cc_start: 0.6774 (mtp) cc_final: 0.6477 (ttm) REVERT: A 265 HIS cc_start: 0.8110 (p-80) cc_final: 0.7661 (p90) REVERT: A 383 MET cc_start: 0.8693 (ttt) cc_final: 0.8384 (ttt) REVERT: A 557 MET cc_start: 0.8861 (tmm) cc_final: 0.8622 (tmm) REVERT: E 347 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6294 (m-80) REVERT: E 357 ARG cc_start: 0.8546 (ttt90) cc_final: 0.6465 (mtt180) REVERT: E 424 LYS cc_start: 0.8848 (tptp) cc_final: 0.8401 (tttp) REVERT: E 451 TYR cc_start: 0.8006 (m-80) cc_final: 0.6886 (m-80) REVERT: E 462 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8387 (mtpp) REVERT: E 467 ASP cc_start: 0.7803 (t0) cc_final: 0.7312 (t70) REVERT: E 495 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.8115 (p90) REVERT: E 508 TYR cc_start: 0.8363 (m-80) cc_final: 0.7953 (m-80) outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.2102 time to fit residues: 27.4958 Evaluate side-chains 87 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.143048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113821 restraints weight = 20231.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.116757 restraints weight = 13366.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.117282 restraints weight = 9279.358| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6637 Z= 0.147 Angle : 0.641 7.628 9025 Z= 0.325 Chirality : 0.043 0.206 944 Planarity : 0.005 0.058 1167 Dihedral : 6.470 56.614 932 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.89 % Favored : 90.98 % Rotamer: Outliers : 2.18 % Allowed : 12.50 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.26 % 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: -2.05 (0.29), residues: 788 helix: -0.01 (0.27), residues: 369 sheet: -2.12 (0.68), residues: 48 loop : -2.76 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 163 HIS 0.005 0.001 HIS A 378 PHE 0.017 0.002 PHE A 390 TYR 0.019 0.002 TYR A 252 ARG 0.005 0.001 ARG E 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 3) link_NAG-ASN : angle 2.50719 ( 9) hydrogen bonds : bond 0.04552 ( 270) hydrogen bonds : angle 5.02916 ( 788) SS BOND : bond 0.00114 ( 3) SS BOND : angle 1.59367 ( 6) covalent geometry : bond 0.00337 ( 6631) covalent geometry : angle 0.63481 ( 9010) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6569 (mm-40) cc_final: 0.6254 (pp30) REVERT: A 265 HIS cc_start: 0.7943 (p-80) cc_final: 0.7473 (p90) REVERT: A 402 GLU cc_start: 0.6991 (tp30) cc_final: 0.6467 (mp0) REVERT: A 557 MET cc_start: 0.8849 (tmm) cc_final: 0.8642 (tmm) REVERT: A 591 LEU cc_start: 0.8253 (tt) cc_final: 0.7942 (tt) REVERT: E 347 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: E 356 LYS cc_start: 0.8726 (tttt) cc_final: 0.7753 (mmtt) REVERT: E 357 ARG cc_start: 0.8574 (ttt90) cc_final: 0.6473 (mtt180) REVERT: E 424 LYS cc_start: 0.8838 (tptp) cc_final: 0.8321 (tttm) REVERT: E 451 TYR cc_start: 0.8005 (m-80) cc_final: 0.6854 (m-80) REVERT: E 462 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8356 (mtpp) REVERT: E 467 ASP cc_start: 0.7709 (t0) cc_final: 0.7171 (t70) REVERT: E 495 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7978 (p90) REVERT: E 508 TYR cc_start: 0.8222 (m-80) cc_final: 0.7856 (m-80) outliers start: 14 outliers final: 8 residues processed: 111 average time/residue: 0.1927 time to fit residues: 28.2454 Evaluate side-chains 97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.144512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114102 restraints weight = 26554.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.119293 restraints weight = 16601.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.119619 restraints weight = 8675.286| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6637 Z= 0.142 Angle : 0.638 7.164 9025 Z= 0.319 Chirality : 0.043 0.199 944 Planarity : 0.005 0.056 1167 Dihedral : 5.926 56.370 932 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.28 % Favored : 90.60 % Rotamer: Outliers : 2.33 % Allowed : 14.39 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.13 % 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: -1.62 (0.30), residues: 788 helix: 0.28 (0.27), residues: 378 sheet: -2.00 (0.67), residues: 46 loop : -2.50 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.005 0.001 HIS A 378 PHE 0.016 0.002 PHE A 390 TYR 0.015 0.001 TYR E 495 ARG 0.004 0.000 ARG E 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 3) link_NAG-ASN : angle 2.29949 ( 9) hydrogen bonds : bond 0.04196 ( 270) hydrogen bonds : angle 4.88201 ( 788) SS BOND : bond 0.00357 ( 3) SS BOND : angle 1.79353 ( 6) covalent geometry : bond 0.00330 ( 6631) covalent geometry : angle 0.63260 ( 9010) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6579 (mm-40) cc_final: 0.6302 (pp30) REVERT: A 265 HIS cc_start: 0.7916 (p-80) cc_final: 0.7519 (p90) REVERT: A 270 MET cc_start: 0.6027 (tpp) cc_final: 0.5132 (tpp) REVERT: A 402 GLU cc_start: 0.7093 (tp30) cc_final: 0.6579 (mp0) REVERT: A 591 LEU cc_start: 0.8256 (tt) cc_final: 0.7941 (tt) REVERT: E 347 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6209 (m-80) REVERT: E 356 LYS cc_start: 0.8660 (tttt) cc_final: 0.7746 (mmtt) REVERT: E 357 ARG cc_start: 0.8559 (ttt90) cc_final: 0.6429 (mtt180) REVERT: E 424 LYS cc_start: 0.8852 (tptp) cc_final: 0.8361 (tttm) REVERT: E 451 TYR cc_start: 0.7998 (m-80) cc_final: 0.6948 (m-80) REVERT: E 462 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8320 (mtpp) REVERT: E 495 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.8098 (p90) REVERT: E 508 TYR cc_start: 0.8249 (m-80) cc_final: 0.7883 (m-80) outliers start: 15 outliers final: 7 residues processed: 101 average time/residue: 0.2104 time to fit residues: 27.6402 Evaluate side-chains 92 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.144805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.115333 restraints weight = 20199.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.119841 restraints weight = 12603.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.119871 restraints weight = 8827.133| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6637 Z= 0.139 Angle : 0.637 7.052 9025 Z= 0.317 Chirality : 0.043 0.197 944 Planarity : 0.005 0.055 1167 Dihedral : 5.597 55.945 932 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.39 % Favored : 91.49 % Rotamer: Outliers : 2.47 % Allowed : 15.12 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.48 (0.30), residues: 788 helix: 0.32 (0.27), residues: 382 sheet: -1.78 (0.70), residues: 46 loop : -2.38 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 378 PHE 0.016 0.002 PHE A 512 TYR 0.019 0.001 TYR A 50 ARG 0.005 0.000 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 3) link_NAG-ASN : angle 2.24277 ( 9) hydrogen bonds : bond 0.04196 ( 270) hydrogen bonds : angle 4.85774 ( 788) SS BOND : bond 0.00120 ( 3) SS BOND : angle 1.72113 ( 6) covalent geometry : bond 0.00324 ( 6631) covalent geometry : angle 0.63167 ( 9010) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6612 (mm-40) cc_final: 0.6344 (pp30) REVERT: A 249 MET cc_start: 0.8032 (tpp) cc_final: 0.7760 (tpp) REVERT: A 265 HIS cc_start: 0.8048 (p-80) cc_final: 0.7766 (p90) REVERT: A 267 LEU cc_start: 0.8444 (mt) cc_final: 0.7801 (mt) REVERT: A 402 GLU cc_start: 0.6871 (tp30) cc_final: 0.6557 (mp0) REVERT: A 591 LEU cc_start: 0.8197 (tt) cc_final: 0.7874 (tt) REVERT: E 347 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6136 (m-80) REVERT: E 356 LYS cc_start: 0.8622 (tttt) cc_final: 0.7666 (mmtt) REVERT: E 357 ARG cc_start: 0.8566 (ttt90) cc_final: 0.6426 (mtt180) REVERT: E 424 LYS cc_start: 0.8846 (tptp) cc_final: 0.8321 (tttm) REVERT: E 451 TYR cc_start: 0.7943 (m-80) cc_final: 0.6877 (m-80) REVERT: E 462 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8266 (mtpp) REVERT: E 495 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.8079 (p90) REVERT: E 508 TYR cc_start: 0.8283 (m-80) cc_final: 0.7868 (m-80) REVERT: E 515 PHE cc_start: 0.7027 (m-80) cc_final: 0.6801 (m-80) outliers start: 16 outliers final: 11 residues processed: 102 average time/residue: 0.2124 time to fit residues: 28.2749 Evaluate side-chains 97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.142839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113297 restraints weight = 22107.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118318 restraints weight = 13260.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.117913 restraints weight = 9722.277| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6637 Z= 0.173 Angle : 0.668 7.676 9025 Z= 0.331 Chirality : 0.043 0.200 944 Planarity : 0.005 0.053 1167 Dihedral : 5.667 56.177 932 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.28 % Favored : 90.60 % Rotamer: Outliers : 2.33 % Allowed : 16.42 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.13 % 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: -1.45 (0.30), residues: 788 helix: 0.32 (0.27), residues: 379 sheet: -1.50 (0.73), residues: 46 loop : -2.36 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.006 0.001 HIS A 378 PHE 0.019 0.002 PHE A 390 TYR 0.018 0.002 TYR E 495 ARG 0.005 0.001 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 3) link_NAG-ASN : angle 2.35638 ( 9) hydrogen bonds : bond 0.04354 ( 270) hydrogen bonds : angle 4.91504 ( 788) SS BOND : bond 0.00166 ( 3) SS BOND : angle 1.78927 ( 6) covalent geometry : bond 0.00409 ( 6631) covalent geometry : angle 0.66309 ( 9010) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.758 Fit side-chains REVERT: A 139 GLN cc_start: 0.6695 (mm-40) cc_final: 0.6443 (pp30) REVERT: A 148 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7379 (mt) REVERT: A 249 MET cc_start: 0.8004 (tpp) cc_final: 0.7588 (tpp) REVERT: A 265 HIS cc_start: 0.8053 (p-80) cc_final: 0.7649 (p90) REVERT: A 267 LEU cc_start: 0.8430 (mt) cc_final: 0.7774 (mt) REVERT: A 402 GLU cc_start: 0.7246 (tp30) cc_final: 0.6686 (mp0) REVERT: A 474 MET cc_start: 0.6881 (mmp) cc_final: 0.6608 (mmp) REVERT: A 489 GLU cc_start: 0.7361 (pt0) cc_final: 0.6473 (pt0) REVERT: E 347 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6168 (m-80) REVERT: E 356 LYS cc_start: 0.8582 (tttt) cc_final: 0.7607 (mmtt) REVERT: E 357 ARG cc_start: 0.8587 (ttt90) cc_final: 0.6524 (mtt180) REVERT: E 424 LYS cc_start: 0.8892 (tptp) cc_final: 0.8360 (tttm) REVERT: E 451 TYR cc_start: 0.7995 (m-80) cc_final: 0.6921 (m-80) REVERT: E 462 LYS cc_start: 0.8616 (mtpt) cc_final: 0.8333 (mtpp) REVERT: E 495 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.8142 (p90) REVERT: E 508 TYR cc_start: 0.8329 (m-80) cc_final: 0.7964 (m-80) REVERT: E 516 GLU cc_start: 0.6791 (pm20) cc_final: 0.6440 (pm20) outliers start: 15 outliers final: 11 residues processed: 98 average time/residue: 0.2075 time to fit residues: 26.6691 Evaluate side-chains 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 0.0030 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.147504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.118333 restraints weight = 26348.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.123761 restraints weight = 16165.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124592 restraints weight = 8562.424| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6637 Z= 0.119 Angle : 0.621 7.797 9025 Z= 0.307 Chirality : 0.042 0.196 944 Planarity : 0.005 0.052 1167 Dihedral : 5.318 55.237 932 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.18 % Allowed : 17.15 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.17 (0.30), residues: 788 helix: 0.50 (0.27), residues: 380 sheet: -1.29 (0.74), residues: 46 loop : -2.16 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.004 0.001 HIS A 378 PHE 0.011 0.001 PHE A 390 TYR 0.016 0.001 TYR A 50 ARG 0.006 0.001 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 3) link_NAG-ASN : angle 2.02206 ( 9) hydrogen bonds : bond 0.03831 ( 270) hydrogen bonds : angle 4.72111 ( 788) SS BOND : bond 0.00121 ( 3) SS BOND : angle 1.61466 ( 6) covalent geometry : bond 0.00272 ( 6631) covalent geometry : angle 0.61684 ( 9010) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 161 ARG cc_start: 0.7119 (mtp180) cc_final: 0.6785 (ttm170) REVERT: A 265 HIS cc_start: 0.8028 (p-80) cc_final: 0.7354 (p90) REVERT: A 267 LEU cc_start: 0.8316 (mt) cc_final: 0.7660 (mt) REVERT: A 402 GLU cc_start: 0.6759 (tp30) cc_final: 0.6295 (mp0) REVERT: A 474 MET cc_start: 0.6640 (mmp) cc_final: 0.6437 (mmp) REVERT: A 480 MET cc_start: 0.8119 (mtp) cc_final: 0.7680 (mtm) REVERT: A 489 GLU cc_start: 0.7341 (pt0) cc_final: 0.6525 (pt0) REVERT: A 557 MET cc_start: 0.8771 (tmm) cc_final: 0.8512 (tmm) REVERT: A 591 LEU cc_start: 0.8174 (tt) cc_final: 0.7830 (tt) REVERT: E 356 LYS cc_start: 0.8413 (tttt) cc_final: 0.7534 (mmtt) REVERT: E 357 ARG cc_start: 0.8597 (ttt90) cc_final: 0.6491 (mtt180) REVERT: E 424 LYS cc_start: 0.8833 (tptp) cc_final: 0.8325 (tttm) REVERT: E 451 TYR cc_start: 0.7822 (m-80) cc_final: 0.6654 (m-80) REVERT: E 462 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8159 (mtpp) REVERT: E 495 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7992 (p90) REVERT: E 508 TYR cc_start: 0.8384 (m-80) cc_final: 0.7982 (m-80) REVERT: E 516 GLU cc_start: 0.6890 (pm20) cc_final: 0.6581 (pm20) outliers start: 14 outliers final: 10 residues processed: 106 average time/residue: 0.2162 time to fit residues: 29.7103 Evaluate side-chains 98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 71 optimal weight: 0.0970 chunk 30 optimal weight: 0.8980 chunk 66 optimal weight: 0.0670 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN ** E 422 ASN ** 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 = 0.4027 r_free = 0.4027 target = 0.149772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.119327 restraints weight = 16817.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120644 restraints weight = 9491.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121552 restraints weight = 8770.492| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6637 Z= 0.117 Angle : 0.618 7.531 9025 Z= 0.305 Chirality : 0.041 0.190 944 Planarity : 0.005 0.052 1167 Dihedral : 5.086 55.010 932 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.60 % Allowed : 18.17 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.01 (0.30), residues: 788 helix: 0.60 (0.27), residues: 382 sheet: -1.11 (0.76), residues: 46 loop : -2.07 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.012 0.001 PHE A 390 TYR 0.019 0.001 TYR A 50 ARG 0.006 0.001 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 3) link_NAG-ASN : angle 1.94793 ( 9) hydrogen bonds : bond 0.03691 ( 270) hydrogen bonds : angle 4.63278 ( 788) SS BOND : bond 0.00090 ( 3) SS BOND : angle 1.60404 ( 6) covalent geometry : bond 0.00264 ( 6631) covalent geometry : angle 0.61383 ( 9010) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 161 ARG cc_start: 0.7206 (mtp180) cc_final: 0.6628 (ttm170) REVERT: A 249 MET cc_start: 0.7804 (tpp) cc_final: 0.7515 (tpp) REVERT: A 265 HIS cc_start: 0.7981 (p-80) cc_final: 0.7219 (p90) REVERT: A 267 LEU cc_start: 0.8212 (mt) cc_final: 0.7589 (mt) REVERT: A 480 MET cc_start: 0.8004 (mtp) cc_final: 0.7567 (mtm) REVERT: A 489 GLU cc_start: 0.7509 (pt0) cc_final: 0.6797 (pt0) REVERT: A 557 MET cc_start: 0.8716 (tmm) cc_final: 0.8492 (tmm) REVERT: A 591 LEU cc_start: 0.8125 (tt) cc_final: 0.7751 (tt) REVERT: E 355 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.7518 (ttt90) REVERT: E 356 LYS cc_start: 0.8287 (tttt) cc_final: 0.7677 (mptt) REVERT: E 357 ARG cc_start: 0.8590 (ttt90) cc_final: 0.6417 (mtt180) REVERT: E 424 LYS cc_start: 0.8797 (tptp) cc_final: 0.8473 (tttm) REVERT: E 451 TYR cc_start: 0.7818 (m-80) cc_final: 0.6876 (m-80) REVERT: E 462 LYS cc_start: 0.8345 (mtpt) cc_final: 0.8105 (mtpp) REVERT: E 474 GLN cc_start: 0.7279 (tt0) cc_final: 0.6857 (pm20) REVERT: E 495 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7961 (p90) REVERT: E 508 TYR cc_start: 0.8307 (m-80) cc_final: 0.7979 (m-80) REVERT: E 516 GLU cc_start: 0.6825 (pm20) cc_final: 0.6566 (pm20) outliers start: 10 outliers final: 5 residues processed: 102 average time/residue: 0.2085 time to fit residues: 27.4953 Evaluate side-chains 95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 0.0770 chunk 64 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 37 optimal weight: 0.0670 chunk 43 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.151892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.120320 restraints weight = 14382.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.122929 restraints weight = 7796.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.123998 restraints weight = 5714.767| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6637 Z= 0.116 Angle : 0.618 7.019 9025 Z= 0.306 Chirality : 0.041 0.191 944 Planarity : 0.005 0.051 1167 Dihedral : 4.802 54.501 930 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.31 % Allowed : 19.48 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.92 (0.30), residues: 788 helix: 0.64 (0.27), residues: 381 sheet: -0.98 (0.77), residues: 46 loop : -1.98 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 477 HIS 0.006 0.001 HIS E 493 PHE 0.011 0.001 PHE A 390 TYR 0.013 0.001 TYR A 385 ARG 0.006 0.000 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 3) link_NAG-ASN : angle 1.82463 ( 9) hydrogen bonds : bond 0.03523 ( 270) hydrogen bonds : angle 4.57062 ( 788) SS BOND : bond 0.00100 ( 3) SS BOND : angle 1.55421 ( 6) covalent geometry : bond 0.00275 ( 6631) covalent geometry : angle 0.61474 ( 9010) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 161 ARG cc_start: 0.7157 (mtp180) cc_final: 0.6602 (ttm170) REVERT: A 249 MET cc_start: 0.7627 (tpp) cc_final: 0.7345 (tpp) REVERT: A 265 HIS cc_start: 0.7943 (p-80) cc_final: 0.7167 (p90) REVERT: A 267 LEU cc_start: 0.8192 (mt) cc_final: 0.7564 (mt) REVERT: A 383 MET cc_start: 0.8550 (ttt) cc_final: 0.8311 (ttm) REVERT: A 402 GLU cc_start: 0.6501 (tp30) cc_final: 0.6293 (mp0) REVERT: A 480 MET cc_start: 0.7899 (mtp) cc_final: 0.7527 (mtm) REVERT: A 489 GLU cc_start: 0.7514 (pt0) cc_final: 0.6778 (pt0) REVERT: E 356 LYS cc_start: 0.8129 (tttt) cc_final: 0.7623 (mptt) REVERT: E 357 ARG cc_start: 0.8534 (ttt90) cc_final: 0.6417 (mtt180) REVERT: E 424 LYS cc_start: 0.8659 (tptp) cc_final: 0.8434 (tttm) REVERT: E 451 TYR cc_start: 0.7761 (m-80) cc_final: 0.6812 (m-80) REVERT: E 462 LYS cc_start: 0.8258 (mtpt) cc_final: 0.8028 (mtpp) REVERT: E 474 GLN cc_start: 0.7313 (tt0) cc_final: 0.6831 (pm20) REVERT: E 508 TYR cc_start: 0.8441 (m-80) cc_final: 0.8109 (m-80) REVERT: E 516 GLU cc_start: 0.6718 (pm20) cc_final: 0.6493 (pm20) outliers start: 8 outliers final: 6 residues processed: 99 average time/residue: 0.1950 time to fit residues: 25.7403 Evaluate side-chains 94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 0.0010 chunk 16 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.148763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116994 restraints weight = 14274.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.120246 restraints weight = 8206.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.121109 restraints weight = 5349.109| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 6637 Z= 0.140 Angle : 0.648 7.432 9025 Z= 0.319 Chirality : 0.042 0.189 944 Planarity : 0.005 0.051 1167 Dihedral : 4.910 54.815 930 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.45 % Allowed : 19.48 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.88 (0.30), residues: 788 helix: 0.65 (0.27), residues: 382 sheet: -0.89 (0.77), residues: 46 loop : -1.96 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 477 HIS 0.006 0.001 HIS E 493 PHE 0.016 0.001 PHE A 390 TYR 0.020 0.001 TYR A 50 ARG 0.007 0.001 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 3) link_NAG-ASN : angle 1.95942 ( 9) hydrogen bonds : bond 0.03748 ( 270) hydrogen bonds : angle 4.62513 ( 788) SS BOND : bond 0.00086 ( 3) SS BOND : angle 1.62086 ( 6) covalent geometry : bond 0.00335 ( 6631) covalent geometry : angle 0.64373 ( 9010) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7350 (mt) REVERT: A 161 ARG cc_start: 0.7177 (mtp180) cc_final: 0.6650 (ttm170) REVERT: A 249 MET cc_start: 0.7621 (tpp) cc_final: 0.7376 (tpp) REVERT: A 265 HIS cc_start: 0.7969 (p-80) cc_final: 0.7189 (p90) REVERT: A 398 GLU cc_start: 0.6942 (pt0) cc_final: 0.6737 (pt0) REVERT: A 402 GLU cc_start: 0.6644 (tp30) cc_final: 0.6409 (mp0) REVERT: A 474 MET cc_start: 0.7530 (mmm) cc_final: 0.7165 (mpp) REVERT: A 480 MET cc_start: 0.7867 (mtp) cc_final: 0.7443 (mtm) REVERT: A 489 GLU cc_start: 0.7526 (pt0) cc_final: 0.7147 (pt0) REVERT: A 557 MET cc_start: 0.8799 (tmm) cc_final: 0.8515 (tmm) REVERT: A 591 LEU cc_start: 0.8189 (tt) cc_final: 0.7830 (tt) REVERT: E 355 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.7478 (ttt90) REVERT: E 356 LYS cc_start: 0.8273 (tttt) cc_final: 0.7590 (mptt) REVERT: E 357 ARG cc_start: 0.8577 (ttt90) cc_final: 0.6432 (mtt180) REVERT: E 424 LYS cc_start: 0.8723 (tptp) cc_final: 0.8391 (tttm) REVERT: E 451 TYR cc_start: 0.7879 (m-80) cc_final: 0.6999 (m-80) REVERT: E 462 LYS cc_start: 0.8368 (mtpt) cc_final: 0.8137 (mtpp) REVERT: E 474 GLN cc_start: 0.7288 (tt0) cc_final: 0.6853 (pm20) REVERT: E 495 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7941 (p90) REVERT: E 508 TYR cc_start: 0.8497 (m-80) cc_final: 0.8183 (m-80) outliers start: 9 outliers final: 6 residues processed: 91 average time/residue: 0.2288 time to fit residues: 27.3227 Evaluate side-chains 95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.0040 chunk 72 optimal weight: 0.0570 chunk 59 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 0.0970 chunk 24 optimal weight: 0.0470 overall best weight: 0.1406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.155257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.123664 restraints weight = 16048.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.127950 restraints weight = 8510.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.128563 restraints weight = 5502.836| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6637 Z= 0.120 Angle : 0.647 10.807 9025 Z= 0.318 Chirality : 0.042 0.229 944 Planarity : 0.005 0.051 1167 Dihedral : 4.709 53.801 930 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.45 % Allowed : 19.62 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.73 (0.31), residues: 788 helix: 0.75 (0.27), residues: 380 sheet: -0.74 (0.77), residues: 46 loop : -1.85 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 477 HIS 0.003 0.001 HIS E 493 PHE 0.012 0.001 PHE A 525 TYR 0.033 0.001 TYR A 50 ARG 0.007 0.001 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 3) link_NAG-ASN : angle 1.59969 ( 9) hydrogen bonds : bond 0.03457 ( 270) hydrogen bonds : angle 4.60899 ( 788) SS BOND : bond 0.00132 ( 3) SS BOND : angle 1.46376 ( 6) covalent geometry : bond 0.00279 ( 6631) covalent geometry : angle 0.64442 ( 9010) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3068.83 seconds wall clock time: 55 minutes 20.53 seconds (3320.53 seconds total)