Starting phenix.real_space_refine on Wed Jun 4 22:20:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9elg_48148/06_2025/9elg_48148.cif Found real_map, /net/cci-nas-00/data/ceres_data/9elg_48148/06_2025/9elg_48148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9elg_48148/06_2025/9elg_48148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9elg_48148/06_2025/9elg_48148.map" model { file = "/net/cci-nas-00/data/ceres_data/9elg_48148/06_2025/9elg_48148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9elg_48148/06_2025/9elg_48148.cif" } resolution = 3.71 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= 0.013 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 15 5.16 5 C 2742 2.51 5 N 688 2.21 5 O 810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4255 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1928 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain breaks: 4 Chain: "C" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2173 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 18, 'TRANS': 253} Chain: "B" 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" 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 Time building chain proxies: 4.77, per 1000 atoms: 1.12 Number of scatterers: 4255 At special positions: 0 Unit cell: (83.288, 89.75, 84.724, 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 15 16.00 O 810 8.00 N 688 7.00 C 2742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 163 " 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 301 " - " ASN A 30 " " NAG A 302 " - " ASN A 61 " " NAG A 303 " - " ASN A 230 " " NAG A 304 " - " ASN A 120 " " NAG A 305 " - " ASN A 162 " " NAG A 306 " - " ASN A 241 " " NAG A 307 " - " ASN A 278 " " NAG B 1 " - " ASN C 354 " " NAG C 601 " - " ASN C 331 " " NAG C 602 " - " ASN C 343 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 478.6 milliseconds 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 958 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 7 sheets defined 8.8% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.505A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.586A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 372 removed outlier: 3.515A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 removed outlier: 4.242A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.795A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 411 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.336A pdb=" N PHE A 198 " --> pdb=" O ASP A 224 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP A 224 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 200 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.566A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.022A pdb=" N ASP A 283 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.568A pdb=" N LEU A 240 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 141 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.070A pdb=" N GLY A 101 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA A 239 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE A 99 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLU A 130 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS A 163 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN A 132 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N ASN A 161 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'C' and resid 391 through 392 124 hydrogen bonds defined for protein. 306 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: 1.12 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 667 1.31 - 1.44: 1307 1.44 - 1.56: 2377 1.56 - 1.69: 3 1.69 - 1.82: 16 Bond restraints: 4370 Sorted by residual: bond pdb=" CA THR A 29 " pdb=" C THR A 29 " ideal model delta sigma weight residual 1.523 1.432 0.092 1.28e-02 6.10e+03 5.12e+01 bond pdb=" CA PHE A 32 " pdb=" C PHE A 32 " ideal model delta sigma weight residual 1.521 1.452 0.069 1.17e-02 7.31e+03 3.52e+01 bond pdb=" C PHE A 32 " pdb=" O PHE A 32 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.14e-02 7.69e+03 1.92e+01 bond pdb=" C THR A 29 " pdb=" O THR A 29 " ideal model delta sigma weight residual 1.237 1.183 0.054 1.39e-02 5.18e+03 1.50e+01 bond pdb=" C THR A 29 " pdb=" N ASN A 30 " ideal model delta sigma weight residual 1.335 1.268 0.067 1.86e-02 2.89e+03 1.31e+01 ... (remaining 4365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 5755 3.14 - 6.27: 160 6.27 - 9.41: 17 9.41 - 12.55: 8 12.55 - 15.69: 1 Bond angle restraints: 5941 Sorted by residual: angle pdb=" C THR A 29 " pdb=" N ASN A 30 " pdb=" CA ASN A 30 " ideal model delta sigma weight residual 123.03 107.34 15.69 1.34e+00 5.57e-01 1.37e+02 angle pdb=" CA PHE A 32 " pdb=" CB PHE A 32 " pdb=" CG PHE A 32 " ideal model delta sigma weight residual 113.80 122.82 -9.02 1.00e+00 1.00e+00 8.13e+01 angle pdb=" CA PRO C 589 " pdb=" N PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 112.00 100.80 11.20 1.40e+00 5.10e-01 6.40e+01 angle pdb=" CA THR A 33 " pdb=" CB THR A 33 " pdb=" OG1 THR A 33 " ideal model delta sigma weight residual 109.60 99.45 10.15 1.50e+00 4.44e-01 4.58e+01 angle pdb=" N PHE A 32 " pdb=" CA PHE A 32 " pdb=" CB PHE A 32 " ideal model delta sigma weight residual 110.65 101.83 8.82 1.56e+00 4.11e-01 3.20e+01 ... (remaining 5936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.46: 2592 25.46 - 50.91: 87 50.91 - 76.36: 22 76.36 - 101.82: 2 101.82 - 127.27: 3 Dihedral angle restraints: 2706 sinusoidal: 1215 harmonic: 1491 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -170.09 84.09 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CD ARG A 76 " pdb=" NE ARG A 76 " pdb=" CZ ARG A 76 " pdb=" NH1 ARG A 76 " ideal model delta sinusoidal sigma weight residual 0.00 54.52 -54.52 1 1.00e+01 1.00e-02 4.03e+01 dihedral pdb=" N THR A 29 " pdb=" C THR A 29 " pdb=" CA THR A 29 " pdb=" CB THR A 29 " ideal model delta harmonic sigma weight residual 123.40 109.20 14.20 0 2.50e+00 1.60e-01 3.23e+01 ... (remaining 2703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.316: 673 0.316 - 0.632: 2 0.632 - 0.949: 0 0.949 - 1.265: 0 1.265 - 1.581: 1 Chirality restraints: 676 Sorted by residual: chirality pdb=" C1 NAG A 307 " pdb=" ND2 ASN A 278 " pdb=" C2 NAG A 307 " pdb=" O5 NAG A 307 " both_signs ideal model delta sigma weight residual False -2.40 -0.82 -1.58 2.00e-01 2.50e+01 6.25e+01 chirality pdb=" C1 NAG A 302 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A 302 " pdb=" O5 NAG A 302 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" CA ASN A 30 " pdb=" N ASN A 30 " pdb=" C ASN A 30 " pdb=" CB ASN A 30 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 673 not shown) Planarity restraints: 760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 301 " -0.156 2.00e-02 2.50e+03 1.31e-01 2.16e+02 pdb=" C7 NAG A 301 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG A 301 " -0.112 2.00e-02 2.50e+03 pdb=" N2 NAG A 301 " 0.219 2.00e-02 2.50e+03 pdb=" O7 NAG A 301 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 76 " -0.750 9.50e-02 1.11e+02 3.37e-01 7.76e+01 pdb=" NE ARG A 76 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 76 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG A 76 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 76 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 588 " -0.127 5.00e-02 4.00e+02 1.84e-01 5.39e+01 pdb=" N PRO C 589 " 0.317 5.00e-02 4.00e+02 pdb=" CA PRO C 589 " -0.100 5.00e-02 4.00e+02 pdb=" CD PRO C 589 " -0.090 5.00e-02 4.00e+02 ... (remaining 757 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 43 2.58 - 3.16: 3367 3.16 - 3.74: 6091 3.74 - 4.32: 8918 4.32 - 4.90: 14637 Nonbonded interactions: 33056 Sorted by model distance: nonbonded pdb=" O GLN A 52 " pdb=" OD1 ASP A 53 " model vdw 2.006 3.040 nonbonded pdb=" OH TYR C 453 " pdb=" OE1 GLU C 493 " model vdw 2.154 3.040 nonbonded pdb=" OH TYR A 89 " pdb=" OE2 GLU A 188 " model vdw 2.237 3.040 nonbonded pdb=" N THR A 33 " pdb=" OG1 THR A 33 " model vdw 2.286 2.496 nonbonded pdb=" NZ LYS A 75 " pdb=" OD1 ASN A 79 " model vdw 2.321 3.120 ... (remaining 33051 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=1.00 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: 8.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.110 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 0.098 4387 Z= 0.369 Angle : 1.334 15.686 5986 Z= 0.745 Chirality : 0.091 1.581 676 Planarity : 0.017 0.337 750 Dihedral : 13.819 127.274 1730 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.35), residues: 498 helix: -2.83 (0.87), residues: 19 sheet: 1.28 (0.41), residues: 147 loop : -0.08 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 452 HIS 0.004 0.001 HIS C 445 PHE 0.073 0.004 PHE C 565 TYR 0.036 0.004 TYR C 380 ARG 0.051 0.002 ARG A 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 10) link_NAG-ASN : angle 5.37829 ( 30) link_BETA1-4 : bond 0.00030 ( 1) link_BETA1-4 : angle 0.46197 ( 3) hydrogen bonds : bond 0.11458 ( 122) hydrogen bonds : angle 8.74567 ( 306) SS BOND : bond 0.00524 ( 6) SS BOND : angle 2.66947 ( 12) covalent geometry : bond 0.00755 ( 4370) covalent geometry : angle 1.27799 ( 5941) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.408 Fit side-chains REVERT: A 30 ASN cc_start: 0.8184 (p0) cc_final: 0.7810 (p0) REVERT: A 33 THR cc_start: 0.8215 (p) cc_final: 0.7967 (p) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1472 time to fit residues: 13.4802 Evaluate side-chains 53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 113 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 235 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.193895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.159745 restraints weight = 4936.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.161680 restraints weight = 4134.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.163611 restraints weight = 3265.663| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4387 Z= 0.175 Angle : 0.729 12.518 5986 Z= 0.368 Chirality : 0.051 0.332 676 Planarity : 0.007 0.097 750 Dihedral : 9.682 81.024 786 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.32 % Allowed : 11.23 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.36), residues: 498 helix: -2.21 (0.86), residues: 28 sheet: 1.04 (0.40), residues: 148 loop : -0.09 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.003 0.001 HIS A 204 PHE 0.021 0.002 PHE A 131 TYR 0.018 0.002 TYR A 261 ARG 0.004 0.001 ARG A 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00756 ( 10) link_NAG-ASN : angle 3.55105 ( 30) link_BETA1-4 : bond 0.00168 ( 1) link_BETA1-4 : angle 0.93433 ( 3) hydrogen bonds : bond 0.04075 ( 122) hydrogen bonds : angle 7.14194 ( 306) SS BOND : bond 0.00114 ( 6) SS BOND : angle 1.15644 ( 12) covalent geometry : bond 0.00406 ( 4370) covalent geometry : angle 0.68453 ( 5941) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7854 (p) cc_final: 0.7614 (p) REVERT: C 452 TRP cc_start: 0.8130 (m100) cc_final: 0.7849 (m-10) outliers start: 6 outliers final: 5 residues processed: 66 average time/residue: 0.1488 time to fit residues: 13.0682 Evaluate side-chains 61 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 445 HIS ** C 487 ASN ** 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 = 0.4118 r_free = 0.4118 target = 0.190404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.156770 restraints weight = 4983.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.157130 restraints weight = 4290.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.160157 restraints weight = 3774.855| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4387 Z= 0.175 Angle : 0.675 11.759 5986 Z= 0.341 Chirality : 0.049 0.296 676 Planarity : 0.006 0.073 750 Dihedral : 9.315 74.222 786 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.76 % Allowed : 11.23 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.36), residues: 498 helix: -2.64 (0.74), residues: 28 sheet: 0.92 (0.40), residues: 149 loop : -0.18 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 452 HIS 0.003 0.001 HIS A 204 PHE 0.015 0.002 PHE A 271 TYR 0.020 0.002 TYR A 261 ARG 0.002 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00838 ( 10) link_NAG-ASN : angle 3.49205 ( 30) link_BETA1-4 : bond 0.00378 ( 1) link_BETA1-4 : angle 0.96267 ( 3) hydrogen bonds : bond 0.03628 ( 122) hydrogen bonds : angle 6.76352 ( 306) SS BOND : bond 0.00309 ( 6) SS BOND : angle 1.17643 ( 12) covalent geometry : bond 0.00396 ( 4370) covalent geometry : angle 0.62814 ( 5941) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.411 Fit side-chains REVERT: A 30 ASN cc_start: 0.7471 (p0) cc_final: 0.6965 (p0) REVERT: A 32 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8864 (m-80) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.1461 time to fit residues: 11.9525 Evaluate side-chains 62 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 445 HIS Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** 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 = 0.4087 r_free = 0.4087 target = 0.187001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151932 restraints weight = 5020.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.153423 restraints weight = 4367.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156292 restraints weight = 3491.912| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4387 Z= 0.204 Angle : 0.696 11.332 5986 Z= 0.347 Chirality : 0.050 0.298 676 Planarity : 0.005 0.063 750 Dihedral : 8.866 68.925 786 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.42 % Allowed : 13.00 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.36), residues: 498 helix: -2.50 (0.84), residues: 21 sheet: 0.64 (0.40), residues: 150 loop : -0.41 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.008 0.001 HIS C 445 PHE 0.012 0.002 PHE A 90 TYR 0.022 0.002 TYR A 261 ARG 0.003 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 10) link_NAG-ASN : angle 3.97226 ( 30) link_BETA1-4 : bond 0.00185 ( 1) link_BETA1-4 : angle 0.81801 ( 3) hydrogen bonds : bond 0.03491 ( 122) hydrogen bonds : angle 6.69737 ( 306) SS BOND : bond 0.00285 ( 6) SS BOND : angle 1.28013 ( 12) covalent geometry : bond 0.00468 ( 4370) covalent geometry : angle 0.63668 ( 5941) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.419 Fit side-chains REVERT: A 30 ASN cc_start: 0.7436 (p0) cc_final: 0.6972 (p0) REVERT: A 32 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8901 (m-80) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.1362 time to fit residues: 12.4094 Evaluate side-chains 67 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** 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 = 0.4149 r_free = 0.4149 target = 0.192778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.160105 restraints weight = 4943.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.160920 restraints weight = 3956.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.162500 restraints weight = 3320.043| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4387 Z= 0.168 Angle : 0.648 10.862 5986 Z= 0.326 Chirality : 0.049 0.303 676 Planarity : 0.005 0.057 750 Dihedral : 8.226 66.775 786 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.20 % Allowed : 14.98 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.36), residues: 498 helix: -2.49 (0.87), residues: 21 sheet: 0.49 (0.40), residues: 151 loop : -0.51 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 353 HIS 0.003 0.001 HIS C 445 PHE 0.012 0.002 PHE A 90 TYR 0.019 0.002 TYR A 261 ARG 0.002 0.000 ARG A 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 10) link_NAG-ASN : angle 3.33572 ( 30) link_BETA1-4 : bond 0.00302 ( 1) link_BETA1-4 : angle 0.74608 ( 3) hydrogen bonds : bond 0.03338 ( 122) hydrogen bonds : angle 6.59999 ( 306) SS BOND : bond 0.00222 ( 6) SS BOND : angle 1.34148 ( 12) covalent geometry : bond 0.00383 ( 4370) covalent geometry : angle 0.60213 ( 5941) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.424 Fit side-chains REVERT: A 30 ASN cc_start: 0.7438 (p0) cc_final: 0.6974 (p0) REVERT: A 32 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8801 (m-80) outliers start: 10 outliers final: 8 residues processed: 63 average time/residue: 0.1608 time to fit residues: 12.9195 Evaluate side-chains 58 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 113 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.195329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.160021 restraints weight = 4947.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.163167 restraints weight = 3746.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165436 restraints weight = 3101.950| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4387 Z= 0.172 Angle : 0.642 10.327 5986 Z= 0.323 Chirality : 0.049 0.305 676 Planarity : 0.005 0.054 750 Dihedral : 7.641 66.083 786 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.42 % Allowed : 15.42 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.36), residues: 498 helix: -2.65 (0.85), residues: 21 sheet: 0.28 (0.40), residues: 153 loop : -0.61 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 452 HIS 0.002 0.001 HIS A 204 PHE 0.011 0.002 PHE A 90 TYR 0.018 0.002 TYR A 261 ARG 0.002 0.000 ARG C 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 10) link_NAG-ASN : angle 3.14761 ( 30) link_BETA1-4 : bond 0.00221 ( 1) link_BETA1-4 : angle 0.67846 ( 3) hydrogen bonds : bond 0.03295 ( 122) hydrogen bonds : angle 6.44291 ( 306) SS BOND : bond 0.00205 ( 6) SS BOND : angle 1.14599 ( 12) covalent geometry : bond 0.00395 ( 4370) covalent geometry : angle 0.60189 ( 5941) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.427 Fit side-chains REVERT: A 30 ASN cc_start: 0.7419 (p0) cc_final: 0.6999 (p0) REVERT: A 32 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8841 (m-80) outliers start: 11 outliers final: 10 residues processed: 70 average time/residue: 0.1552 time to fit residues: 14.0876 Evaluate side-chains 68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 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 = 0.4166 r_free = 0.4166 target = 0.194756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.160679 restraints weight = 4934.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.163531 restraints weight = 3734.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.165945 restraints weight = 3089.008| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4387 Z= 0.156 Angle : 0.627 9.915 5986 Z= 0.317 Chirality : 0.048 0.304 676 Planarity : 0.005 0.052 750 Dihedral : 7.130 63.263 786 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.30 % Allowed : 15.86 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.36), residues: 498 helix: -2.55 (0.87), residues: 21 sheet: 0.29 (0.40), residues: 152 loop : -0.63 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 353 HIS 0.002 0.001 HIS A 204 PHE 0.023 0.002 PHE A 131 TYR 0.017 0.001 TYR A 261 ARG 0.002 0.000 ARG C 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 10) link_NAG-ASN : angle 2.97855 ( 30) link_BETA1-4 : bond 0.00266 ( 1) link_BETA1-4 : angle 0.67709 ( 3) hydrogen bonds : bond 0.03136 ( 122) hydrogen bonds : angle 6.35306 ( 306) SS BOND : bond 0.00181 ( 6) SS BOND : angle 1.20964 ( 12) covalent geometry : bond 0.00358 ( 4370) covalent geometry : angle 0.59033 ( 5941) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8859 (m-80) outliers start: 15 outliers final: 12 residues processed: 71 average time/residue: 0.1658 time to fit residues: 15.3635 Evaluate side-chains 71 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 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 = 0.4129 r_free = 0.4129 target = 0.190410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.155437 restraints weight = 4895.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.158590 restraints weight = 3729.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.160826 restraints weight = 3084.138| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4387 Z= 0.193 Angle : 0.644 9.485 5986 Z= 0.330 Chirality : 0.049 0.298 676 Planarity : 0.005 0.052 750 Dihedral : 7.015 65.016 786 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.52 % Allowed : 15.64 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.36), residues: 498 helix: -2.63 (0.90), residues: 21 sheet: 0.13 (0.40), residues: 152 loop : -0.74 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.003 0.001 HIS A 204 PHE 0.012 0.002 PHE A 90 TYR 0.020 0.002 TYR A 261 ARG 0.003 0.000 ARG C 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 10) link_NAG-ASN : angle 2.90391 ( 30) link_BETA1-4 : bond 0.00158 ( 1) link_BETA1-4 : angle 0.62598 ( 3) hydrogen bonds : bond 0.03244 ( 122) hydrogen bonds : angle 6.49715 ( 306) SS BOND : bond 0.00239 ( 6) SS BOND : angle 1.33032 ( 12) covalent geometry : bond 0.00443 ( 4370) covalent geometry : angle 0.60994 ( 5941) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8900 (m-80) outliers start: 16 outliers final: 13 residues processed: 67 average time/residue: 0.1476 time to fit residues: 12.9653 Evaluate side-chains 71 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 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 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.190905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.156502 restraints weight = 4944.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.159564 restraints weight = 3776.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.161546 restraints weight = 3126.881| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4387 Z= 0.159 Angle : 0.624 9.240 5986 Z= 0.321 Chirality : 0.048 0.303 676 Planarity : 0.005 0.051 750 Dihedral : 6.661 62.477 786 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.52 % Allowed : 16.52 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.36), residues: 498 helix: -2.46 (0.93), residues: 21 sheet: 0.04 (0.40), residues: 152 loop : -0.74 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 452 HIS 0.002 0.001 HIS A 204 PHE 0.012 0.002 PHE C 565 TYR 0.018 0.001 TYR A 261 ARG 0.002 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 10) link_NAG-ASN : angle 2.77418 ( 30) link_BETA1-4 : bond 0.00334 ( 1) link_BETA1-4 : angle 0.65744 ( 3) hydrogen bonds : bond 0.03093 ( 122) hydrogen bonds : angle 6.33604 ( 306) SS BOND : bond 0.00246 ( 6) SS BOND : angle 1.23090 ( 12) covalent geometry : bond 0.00364 ( 4370) covalent geometry : angle 0.59229 ( 5941) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 32 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8828 (m-80) outliers start: 16 outliers final: 14 residues processed: 65 average time/residue: 0.1538 time to fit residues: 13.1540 Evaluate side-chains 71 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 0.0770 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.194791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.161807 restraints weight = 4873.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.164870 restraints weight = 3657.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167093 restraints weight = 3005.055| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4387 Z= 0.132 Angle : 0.591 9.092 5986 Z= 0.304 Chirality : 0.047 0.300 676 Planarity : 0.005 0.052 750 Dihedral : 6.182 58.904 786 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.86 % Allowed : 17.40 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.73 (0.37), residues: 498 helix: -2.43 (0.96), residues: 21 sheet: 0.18 (0.40), residues: 150 loop : -0.66 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 452 HIS 0.002 0.001 HIS A 204 PHE 0.021 0.002 PHE A 77 TYR 0.017 0.001 TYR A 261 ARG 0.001 0.000 ARG C 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 10) link_NAG-ASN : angle 2.65181 ( 30) link_BETA1-4 : bond 0.00353 ( 1) link_BETA1-4 : angle 0.66458 ( 3) hydrogen bonds : bond 0.02965 ( 122) hydrogen bonds : angle 6.14391 ( 306) SS BOND : bond 0.00161 ( 6) SS BOND : angle 1.14647 ( 12) covalent geometry : bond 0.00302 ( 4370) covalent geometry : angle 0.55964 ( 5941) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.467 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 64 average time/residue: 0.1485 time to fit residues: 12.4945 Evaluate side-chains 67 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.190115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156065 restraints weight = 4921.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.159033 restraints weight = 3786.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.161234 restraints weight = 3145.906| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4387 Z= 0.173 Angle : 0.633 9.317 5986 Z= 0.325 Chirality : 0.048 0.289 676 Planarity : 0.005 0.053 750 Dihedral : 6.235 62.092 786 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.74 % Allowed : 16.74 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.36), residues: 498 helix: -2.51 (0.94), residues: 21 sheet: 0.03 (0.40), residues: 151 loop : -0.79 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 353 HIS 0.002 0.001 HIS C 339 PHE 0.022 0.002 PHE A 77 TYR 0.019 0.002 TYR A 261 ARG 0.002 0.000 ARG C 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 10) link_NAG-ASN : angle 3.14385 ( 30) link_BETA1-4 : bond 0.00431 ( 1) link_BETA1-4 : angle 0.62960 ( 3) hydrogen bonds : bond 0.03251 ( 122) hydrogen bonds : angle 6.32107 ( 306) SS BOND : bond 0.00218 ( 6) SS BOND : angle 1.21800 ( 12) covalent geometry : bond 0.00398 ( 4370) covalent geometry : angle 0.59248 ( 5941) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2027.60 seconds wall clock time: 35 minutes 44.36 seconds (2144.36 seconds total)