Starting phenix.real_space_refine on Sun Apr 5 05:06:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ohk_70496/04_2026/9ohk_70496.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ohk_70496/04_2026/9ohk_70496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ohk_70496/04_2026/9ohk_70496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ohk_70496/04_2026/9ohk_70496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ohk_70496/04_2026/9ohk_70496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ohk_70496/04_2026/9ohk_70496.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 60 5.16 5 C 5214 2.51 5 N 1320 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8124 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2580 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 313} Chain: "A" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 128 Unusual residues: {'NAG': 3, 'SVR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C Time building chain proxies: 2.04, per 1000 atoms: 0.25 Number of scatterers: 8124 At special positions: 0 Unit cell: (84.048, 89.816, 126.896, 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 60 16.00 O 1530 8.00 N 1320 7.00 C 5214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 279 " 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 501 " - " ASN A 133 " " NAG A 502 " - " ASN A 194 " " NAG A 503 " - " ASN A 310 " " NAG B 501 " - " ASN B 133 " " NAG B 502 " - " ASN B 194 " " NAG B 503 " - " ASN B 310 " " NAG C 501 " - " ASN C 133 " " NAG C 502 " - " ASN C 194 " " NAG C 503 " - " ASN C 310 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 284.2 milliseconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1806 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 9 sheets defined 22.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 39 through 59 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 337 through 367 removed outlier: 3.782A pdb=" N THR A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 365 " --> pdb=" O TRP A 361 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 59 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 337 through 367 removed outlier: 3.782A pdb=" N THR B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 365 " --> pdb=" O TRP B 361 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 59 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 337 through 367 removed outlier: 3.782A pdb=" N THR C 341 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 365 " --> pdb=" O TRP C 361 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 366 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 72 current: chain 'A' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 176 current: chain 'A' and resid 281 through 286 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 281 through 286 current: chain 'A' and resid 312 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 83 removed outlier: 3.621A pdb=" N LEU A 198 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 removed outlier: 3.532A pdb=" N LYS A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 72 current: chain 'B' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 176 current: chain 'B' and resid 281 through 286 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 281 through 286 current: chain 'B' and resid 312 through 336 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 78 through 83 removed outlier: 3.621A pdb=" N LEU B 198 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.532A pdb=" N LYS B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 72 current: chain 'C' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 168 through 176 current: chain 'C' and resid 281 through 286 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 281 through 286 current: chain 'C' and resid 312 through 336 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 83 removed outlier: 3.621A pdb=" N LEU C 198 " --> pdb=" O LYS C 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 88 removed outlier: 3.531A pdb=" N LYS C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 516 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: 1.09 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1393 1.33 - 1.45: 2368 1.45 - 1.57: 4513 1.57 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 8343 Sorted by residual: bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C1 NAG B 503 " pdb=" O5 NAG B 503 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 8338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 10990 1.89 - 3.78: 287 3.78 - 5.67: 57 5.67 - 7.56: 42 7.56 - 9.45: 6 Bond angle restraints: 11382 Sorted by residual: angle pdb=" CA THR A 196 " pdb=" CB THR A 196 " pdb=" OG1 THR A 196 " ideal model delta sigma weight residual 109.60 102.11 7.49 1.50e+00 4.44e-01 2.50e+01 angle pdb=" CA THR C 196 " pdb=" CB THR C 196 " pdb=" OG1 THR C 196 " ideal model delta sigma weight residual 109.60 102.13 7.47 1.50e+00 4.44e-01 2.48e+01 angle pdb=" CA THR B 196 " pdb=" CB THR B 196 " pdb=" OG1 THR B 196 " ideal model delta sigma weight residual 109.60 102.14 7.46 1.50e+00 4.44e-01 2.48e+01 angle pdb=" C TYR B 98 " pdb=" CA TYR B 98 " pdb=" CB TYR B 98 " ideal model delta sigma weight residual 110.42 119.30 -8.88 1.99e+00 2.53e-01 1.99e+01 angle pdb=" C TYR C 98 " pdb=" CA TYR C 98 " pdb=" CB TYR C 98 " ideal model delta sigma weight residual 110.42 119.28 -8.86 1.99e+00 2.53e-01 1.98e+01 ... (remaining 11377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.58: 4425 24.58 - 49.15: 411 49.15 - 73.72: 45 73.72 - 98.30: 21 98.30 - 122.87: 12 Dihedral angle restraints: 4914 sinusoidal: 2079 harmonic: 2835 Sorted by residual: dihedral pdb=" CB CYS A 226 " pdb=" SG CYS A 226 " pdb=" SG CYS A 236 " pdb=" CB CYS A 236 " ideal model delta sinusoidal sigma weight residual 93.00 52.06 40.94 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" CB CYS B 226 " pdb=" SG CYS B 226 " pdb=" SG CYS B 236 " pdb=" CB CYS B 236 " ideal model delta sinusoidal sigma weight residual 93.00 52.07 40.93 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" CB CYS C 226 " pdb=" SG CYS C 226 " pdb=" SG CYS C 236 " pdb=" CB CYS C 236 " ideal model delta sinusoidal sigma weight residual 93.00 52.08 40.92 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 4911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 749 0.032 - 0.064: 309 0.064 - 0.096: 95 0.096 - 0.128: 79 0.128 - 0.160: 19 Chirality restraints: 1251 Sorted by residual: chirality pdb=" C1 NAG A 503 " pdb=" ND2 ASN A 310 " pdb=" C2 NAG A 503 " pdb=" O5 NAG A 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" C1 NAG C 503 " pdb=" ND2 ASN C 310 " pdb=" C2 NAG C 503 " pdb=" O5 NAG C 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" C1 NAG B 503 " pdb=" ND2 ASN B 310 " pdb=" C2 NAG B 503 " pdb=" O5 NAG B 503 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1248 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 339 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO B 340 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 340 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 340 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 339 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO C 340 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 340 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 340 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 339 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO A 340 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " 0.035 5.00e-02 4.00e+02 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2598 2.82 - 3.34: 7404 3.34 - 3.86: 13198 3.86 - 4.38: 15096 4.38 - 4.90: 26429 Nonbonded interactions: 64725 Sorted by model distance: nonbonded pdb=" O GLY B 84 " pdb=" OH TYR B 98 " model vdw 2.300 3.040 nonbonded pdb=" O GLY A 84 " pdb=" OH TYR A 98 " model vdw 2.300 3.040 nonbonded pdb=" O GLY C 84 " pdb=" OH TYR C 98 " model vdw 2.302 3.040 nonbonded pdb=" N GLU B 89 " pdb=" OE1 GLU B 89 " model vdw 2.306 3.120 nonbonded pdb=" N GLU A 89 " pdb=" OE1 GLU A 89 " model vdw 2.306 3.120 ... (remaining 64720 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 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 : 0.004 0.072 8367 Z= 0.209 Angle : 0.803 9.454 11439 Z= 0.384 Chirality : 0.047 0.160 1251 Planarity : 0.006 0.072 1401 Dihedral : 19.267 122.873 3063 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.35 % Allowed : 35.69 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.27), residues: 981 helix: 1.42 (0.39), residues: 207 sheet: 0.04 (0.29), residues: 342 loop : -1.91 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 218 TYR 0.017 0.001 TYR A 222 PHE 0.008 0.001 PHE C 252 TRP 0.004 0.001 TRP B 175 HIS 0.004 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 8343) covalent geometry : angle 0.80160 (11382) SS BOND : bond 0.00229 ( 15) SS BOND : angle 0.95250 ( 30) hydrogen bonds : bond 0.15904 ( 184) hydrogen bonds : angle 5.35637 ( 516) link_NAG-ASN : bond 0.00346 ( 9) link_NAG-ASN : angle 1.13513 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.311 Fit side-chains REVERT: A 64 GLN cc_start: 0.8686 (tt0) cc_final: 0.8418 (pt0) REVERT: B 64 GLN cc_start: 0.8819 (tt0) cc_final: 0.8566 (pt0) REVERT: C 64 GLN cc_start: 0.8780 (tt0) cc_final: 0.8521 (pt0) outliers start: 3 outliers final: 0 residues processed: 37 average time/residue: 0.0639 time to fit residues: 3.9879 Evaluate side-chains 32 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.092213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.065551 restraints weight = 23773.611| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.73 r_work: 0.3265 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8367 Z= 0.120 Angle : 0.732 9.097 11439 Z= 0.322 Chirality : 0.048 0.165 1251 Planarity : 0.004 0.056 1401 Dihedral : 15.150 110.162 1290 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.77 % Allowed : 30.98 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.27), residues: 981 helix: 1.49 (0.39), residues: 210 sheet: 0.21 (0.30), residues: 324 loop : -1.66 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 218 TYR 0.007 0.001 TYR B 321 PHE 0.012 0.001 PHE C 252 TRP 0.008 0.001 TRP C 361 HIS 0.002 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8343) covalent geometry : angle 0.72719 (11382) SS BOND : bond 0.00211 ( 15) SS BOND : angle 0.80364 ( 30) hydrogen bonds : bond 0.03535 ( 184) hydrogen bonds : angle 3.62275 ( 516) link_NAG-ASN : bond 0.00285 ( 9) link_NAG-ASN : angle 1.79715 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.285 Fit side-chains REVERT: C 367 MET cc_start: 0.7919 (mmp) cc_final: 0.7314 (tpp) outliers start: 15 outliers final: 6 residues processed: 49 average time/residue: 0.0567 time to fit residues: 4.7529 Evaluate side-chains 40 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 0.0770 chunk 14 optimal weight: 5.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS B 64 GLN ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS B 344 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.091683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.065155 restraints weight = 23485.851| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.67 r_work: 0.3230 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8367 Z= 0.122 Angle : 0.717 8.642 11439 Z= 0.312 Chirality : 0.047 0.190 1251 Planarity : 0.004 0.053 1401 Dihedral : 14.525 107.581 1290 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.36 % Allowed : 27.68 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.27), residues: 981 helix: 1.63 (0.38), residues: 210 sheet: -0.08 (0.29), residues: 342 loop : -1.67 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.007 0.001 TYR C 307 PHE 0.010 0.001 PHE C 252 TRP 0.007 0.001 TRP C 361 HIS 0.002 0.000 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8343) covalent geometry : angle 0.71213 (11382) SS BOND : bond 0.00218 ( 15) SS BOND : angle 0.81258 ( 30) hydrogen bonds : bond 0.03218 ( 184) hydrogen bonds : angle 3.40090 ( 516) link_NAG-ASN : bond 0.00261 ( 9) link_NAG-ASN : angle 1.84828 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.322 Fit side-chains REVERT: B 367 MET cc_start: 0.7981 (mmp) cc_final: 0.7650 (tpp) REVERT: C 367 MET cc_start: 0.7994 (mmp) cc_final: 0.7296 (tpp) outliers start: 20 outliers final: 4 residues processed: 56 average time/residue: 0.0884 time to fit residues: 7.0164 Evaluate side-chains 37 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 67 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 292 HIS B 64 GLN ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.090998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.064200 restraints weight = 24101.433| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.83 r_work: 0.3233 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8367 Z= 0.135 Angle : 0.739 9.203 11439 Z= 0.317 Chirality : 0.048 0.175 1251 Planarity : 0.004 0.050 1401 Dihedral : 13.784 104.822 1290 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.65 % Allowed : 28.27 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.27), residues: 981 helix: 1.76 (0.38), residues: 210 sheet: -0.13 (0.29), residues: 342 loop : -1.67 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 218 TYR 0.008 0.001 TYR C 307 PHE 0.010 0.001 PHE C 252 TRP 0.006 0.001 TRP B 361 HIS 0.002 0.000 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8343) covalent geometry : angle 0.73180 (11382) SS BOND : bond 0.00244 ( 15) SS BOND : angle 0.79903 ( 30) hydrogen bonds : bond 0.03032 ( 184) hydrogen bonds : angle 3.23367 ( 516) link_NAG-ASN : bond 0.00190 ( 9) link_NAG-ASN : angle 2.27668 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.260 Fit side-chains REVERT: A 64 GLN cc_start: 0.8959 (pt0) cc_final: 0.8622 (pt0) REVERT: A 367 MET cc_start: 0.7877 (mmp) cc_final: 0.7484 (tpp) REVERT: B 64 GLN cc_start: 0.8905 (pt0) cc_final: 0.8612 (pt0) REVERT: C 64 GLN cc_start: 0.8946 (pt0) cc_final: 0.8528 (pt0) outliers start: 14 outliers final: 5 residues processed: 48 average time/residue: 0.0741 time to fit residues: 5.4245 Evaluate side-chains 40 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 5 optimal weight: 0.1980 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 40.0000 chunk 90 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 89 optimal weight: 0.0770 overall best weight: 2.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.090242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.062683 restraints weight = 23878.521| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.90 r_work: 0.3189 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8367 Z= 0.210 Angle : 0.809 9.119 11439 Z= 0.347 Chirality : 0.049 0.181 1251 Planarity : 0.004 0.045 1401 Dihedral : 12.911 102.259 1290 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.36 % Allowed : 26.86 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.27), residues: 981 helix: 1.39 (0.38), residues: 228 sheet: -0.15 (0.29), residues: 336 loop : -1.62 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 218 TYR 0.013 0.001 TYR C 307 PHE 0.012 0.001 PHE A 252 TRP 0.006 0.001 TRP A 93 HIS 0.002 0.001 HIS C 229 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 8343) covalent geometry : angle 0.79459 (11382) SS BOND : bond 0.00398 ( 15) SS BOND : angle 0.89198 ( 30) hydrogen bonds : bond 0.03360 ( 184) hydrogen bonds : angle 3.33807 ( 516) link_NAG-ASN : bond 0.00212 ( 9) link_NAG-ASN : angle 3.17361 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.320 Fit side-chains REVERT: A 64 GLN cc_start: 0.8872 (pt0) cc_final: 0.8441 (pt0) REVERT: B 64 GLN cc_start: 0.8828 (pt0) cc_final: 0.8528 (pt0) REVERT: C 64 GLN cc_start: 0.8894 (pt0) cc_final: 0.8404 (pt0) outliers start: 20 outliers final: 10 residues processed: 49 average time/residue: 0.0674 time to fit residues: 5.2705 Evaluate side-chains 40 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 215 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.091394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.064476 restraints weight = 23633.985| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.89 r_work: 0.3210 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8367 Z= 0.131 Angle : 0.771 8.553 11439 Z= 0.324 Chirality : 0.047 0.181 1251 Planarity : 0.003 0.041 1401 Dihedral : 12.042 99.277 1290 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.30 % Allowed : 27.80 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.28), residues: 981 helix: 2.09 (0.38), residues: 213 sheet: -0.24 (0.29), residues: 342 loop : -1.65 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 218 TYR 0.008 0.001 TYR C 307 PHE 0.010 0.001 PHE C 252 TRP 0.005 0.001 TRP A 175 HIS 0.002 0.000 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8343) covalent geometry : angle 0.75131 (11382) SS BOND : bond 0.00242 ( 15) SS BOND : angle 0.93274 ( 30) hydrogen bonds : bond 0.03011 ( 184) hydrogen bonds : angle 3.15382 ( 516) link_NAG-ASN : bond 0.00116 ( 9) link_NAG-ASN : angle 3.56727 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.275 Fit side-chains REVERT: A 64 GLN cc_start: 0.8906 (pt0) cc_final: 0.8639 (pt0) REVERT: A 367 MET cc_start: 0.7886 (mmp) cc_final: 0.7675 (tpp) REVERT: B 64 GLN cc_start: 0.8852 (pt0) cc_final: 0.8606 (pt0) REVERT: C 64 GLN cc_start: 0.8932 (pt0) cc_final: 0.8495 (pt0) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.0637 time to fit residues: 4.4876 Evaluate side-chains 39 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS B 292 HIS C 292 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.088640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.060777 restraints weight = 24073.377| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.87 r_work: 0.3111 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 8367 Z= 0.344 Angle : 0.883 8.525 11439 Z= 0.389 Chirality : 0.050 0.208 1251 Planarity : 0.004 0.038 1401 Dihedral : 12.050 97.831 1290 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.77 % Allowed : 26.62 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.27), residues: 981 helix: 1.38 (0.37), residues: 231 sheet: -0.29 (0.29), residues: 327 loop : -1.70 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 113 TYR 0.016 0.002 TYR C 307 PHE 0.014 0.002 PHE B 252 TRP 0.007 0.001 TRP A 93 HIS 0.003 0.001 HIS C 229 Details of bonding type rmsd covalent geometry : bond 0.00801 ( 8343) covalent geometry : angle 0.86351 (11382) SS BOND : bond 0.00627 ( 15) SS BOND : angle 1.06740 ( 30) hydrogen bonds : bond 0.03795 ( 184) hydrogen bonds : angle 3.48966 ( 516) link_NAG-ASN : bond 0.00449 ( 9) link_NAG-ASN : angle 3.83220 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.372 Fit side-chains REVERT: A 64 GLN cc_start: 0.8823 (pt0) cc_final: 0.8392 (pt0) REVERT: A 367 MET cc_start: 0.7955 (mmp) cc_final: 0.7750 (tpp) REVERT: B 64 GLN cc_start: 0.8787 (pt0) cc_final: 0.8535 (pt0) REVERT: C 64 GLN cc_start: 0.8849 (pt0) cc_final: 0.8362 (pt0) outliers start: 15 outliers final: 12 residues processed: 45 average time/residue: 0.0654 time to fit residues: 4.8027 Evaluate side-chains 42 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.089139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.061532 restraints weight = 23417.825| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.66 r_work: 0.3142 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8367 Z= 0.132 Angle : 0.770 9.156 11439 Z= 0.327 Chirality : 0.047 0.178 1251 Planarity : 0.003 0.036 1401 Dihedral : 11.443 94.191 1290 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.41 % Allowed : 27.21 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.28), residues: 981 helix: 1.58 (0.38), residues: 231 sheet: -0.28 (0.29), residues: 339 loop : -1.59 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 218 TYR 0.007 0.001 TYR C 307 PHE 0.011 0.001 PHE B 252 TRP 0.006 0.001 TRP A 175 HIS 0.002 0.000 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8343) covalent geometry : angle 0.75353 (11382) SS BOND : bond 0.00247 ( 15) SS BOND : angle 1.05311 ( 30) hydrogen bonds : bond 0.03099 ( 184) hydrogen bonds : angle 3.16674 ( 516) link_NAG-ASN : bond 0.00156 ( 9) link_NAG-ASN : angle 3.20802 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.336 Fit side-chains REVERT: A 64 GLN cc_start: 0.8909 (pt0) cc_final: 0.8686 (pt0) REVERT: A 367 MET cc_start: 0.7930 (mmp) cc_final: 0.7692 (tpp) REVERT: B 64 GLN cc_start: 0.8838 (pt0) cc_final: 0.8632 (pt0) REVERT: C 64 GLN cc_start: 0.8937 (pt0) cc_final: 0.8513 (pt0) outliers start: 12 outliers final: 10 residues processed: 47 average time/residue: 0.0659 time to fit residues: 5.0070 Evaluate side-chains 43 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 0.0870 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 87 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 292 HIS ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.089817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.062473 restraints weight = 23414.153| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.65 r_work: 0.3162 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8367 Z= 0.116 Angle : 0.756 9.951 11439 Z= 0.318 Chirality : 0.046 0.179 1251 Planarity : 0.004 0.035 1401 Dihedral : 10.810 88.585 1290 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.65 % Allowed : 26.97 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.28), residues: 981 helix: 2.19 (0.38), residues: 213 sheet: -0.28 (0.29), residues: 342 loop : -1.54 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 218 TYR 0.006 0.001 TYR B 307 PHE 0.012 0.001 PHE C 252 TRP 0.005 0.001 TRP A 175 HIS 0.003 0.000 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8343) covalent geometry : angle 0.74186 (11382) SS BOND : bond 0.00195 ( 15) SS BOND : angle 0.96288 ( 30) hydrogen bonds : bond 0.02871 ( 184) hydrogen bonds : angle 3.06967 ( 516) link_NAG-ASN : bond 0.00205 ( 9) link_NAG-ASN : angle 3.02086 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.303 Fit side-chains REVERT: A 64 GLN cc_start: 0.8868 (pt0) cc_final: 0.8660 (pt0) REVERT: A 218 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8553 (mtp85) REVERT: A 367 MET cc_start: 0.7912 (mmp) cc_final: 0.7663 (tpp) REVERT: B 150 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8752 (mt) REVERT: C 56 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: C 64 GLN cc_start: 0.8887 (pt0) cc_final: 0.8477 (pt0) outliers start: 14 outliers final: 9 residues processed: 47 average time/residue: 0.0674 time to fit residues: 5.1068 Evaluate side-chains 43 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 94 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS B 292 HIS ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.089657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.062164 restraints weight = 23304.943| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.66 r_work: 0.3103 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8367 Z= 0.125 Angle : 0.752 9.954 11439 Z= 0.317 Chirality : 0.046 0.163 1251 Planarity : 0.004 0.035 1401 Dihedral : 10.308 80.757 1290 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.41 % Allowed : 27.21 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.28), residues: 981 helix: 2.26 (0.38), residues: 213 sheet: -0.27 (0.29), residues: 342 loop : -1.53 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 218 TYR 0.008 0.001 TYR B 307 PHE 0.010 0.001 PHE C 252 TRP 0.005 0.001 TRP A 175 HIS 0.003 0.000 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8343) covalent geometry : angle 0.73575 (11382) SS BOND : bond 0.00286 ( 15) SS BOND : angle 1.00672 ( 30) hydrogen bonds : bond 0.02907 ( 184) hydrogen bonds : angle 3.02918 ( 516) link_NAG-ASN : bond 0.00190 ( 9) link_NAG-ASN : angle 3.15292 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.302 Fit side-chains REVERT: A 64 GLN cc_start: 0.8820 (pt0) cc_final: 0.8599 (pt0) REVERT: B 50 LEU cc_start: 0.9454 (tt) cc_final: 0.9176 (mm) REVERT: B 150 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8784 (mt) REVERT: C 64 GLN cc_start: 0.8846 (pt0) cc_final: 0.8458 (pt0) outliers start: 12 outliers final: 8 residues processed: 42 average time/residue: 0.0640 time to fit residues: 4.2657 Evaluate side-chains 39 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS B 64 GLN B 292 HIS C 292 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.085855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057015 restraints weight = 23251.260| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.09 r_work: 0.2958 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8367 Z= 0.127 Angle : 0.757 10.031 11439 Z= 0.319 Chirality : 0.045 0.147 1251 Planarity : 0.004 0.035 1401 Dihedral : 9.582 67.098 1290 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.18 % Allowed : 27.44 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.28), residues: 981 helix: 2.30 (0.38), residues: 213 sheet: -0.25 (0.29), residues: 342 loop : -1.55 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 218 TYR 0.007 0.001 TYR B 307 PHE 0.010 0.001 PHE B 252 TRP 0.006 0.001 TRP C 93 HIS 0.002 0.000 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8343) covalent geometry : angle 0.73862 (11382) SS BOND : bond 0.00231 ( 15) SS BOND : angle 0.94234 ( 30) hydrogen bonds : bond 0.02917 ( 184) hydrogen bonds : angle 3.00373 ( 516) link_NAG-ASN : bond 0.00185 ( 9) link_NAG-ASN : angle 3.47717 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2116.48 seconds wall clock time: 36 minutes 59.90 seconds (2219.90 seconds total)