Starting phenix.real_space_refine on Thu Jul 2 04:29:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dv2_27731/07_2026/8dv2_27731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dv2_27731/07_2026/8dv2_27731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dv2_27731/07_2026/8dv2_27731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dv2_27731/07_2026/8dv2_27731.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dv2_27731/07_2026/8dv2_27731.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dv2_27731/07_2026/8dv2_27731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dv2_27731/07_2026/8dv2_27731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dv2_27731/07_2026/8dv2_27731.map" } resolution = 3.5 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4186 2.51 5 N 1075 2.21 5 O 1247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6545 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1590 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.44, per 1000 atoms: 0.22 Number of scatterers: 6545 At special positions: 0 Unit cell: (76.608, 88.704, 122.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1247 8.00 N 1075 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.06 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 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 A1301 " - " ASN A 343 " " NAG D1101 " - " ASN D 322 " " NAG D1102 " - " ASN D 103 " " NAG D1103 " - " ASN D 432 " " NAG D1104 " - " ASN D 546 " " NAG D1105 " - " ASN D 90 " " NAG D1106 " - " ASN D 53 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 357.0 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 57.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.623A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.367A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.645A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'D' and resid 22 through 53 removed outlier: 4.268A pdb=" N ASP D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.605A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 194 Proline residue: D 178 - end of helix removed outlier: 3.790A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 219 through 249 removed outlier: 4.248A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 414 removed outlier: 3.685A pdb=" N THR D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.107A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix removed outlier: 3.617A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.709A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.082A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 350 322 hydrogen bonds defined for protein. 909 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: 0.80 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1305 1.32 - 1.45: 2125 1.45 - 1.58: 3229 1.58 - 1.71: 10 1.71 - 1.84: 58 Bond restraints: 6727 Sorted by residual: bond pdb=" CB HIS D 265 " pdb=" CG HIS D 265 " ideal model delta sigma weight residual 1.497 1.425 0.072 1.40e-02 5.10e+03 2.68e+01 bond pdb=" CB HIS D 535 " pdb=" CG HIS D 535 " ideal model delta sigma weight residual 1.497 1.425 0.072 1.40e-02 5.10e+03 2.64e+01 bond pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 1.516 1.391 0.125 2.50e-02 1.60e+03 2.50e+01 bond pdb=" CZ ARG D 460 " pdb=" NH2 ARG D 460 " ideal model delta sigma weight residual 1.330 1.274 0.056 1.30e-02 5.92e+03 1.83e+01 bond pdb=" CZ ARG D 161 " pdb=" NH2 ARG D 161 " ideal model delta sigma weight residual 1.330 1.278 0.052 1.30e-02 5.92e+03 1.60e+01 ... (remaining 6722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 7882 2.33 - 4.67: 1070 4.67 - 7.00: 171 7.00 - 9.33: 15 9.33 - 11.67: 5 Bond angle restraints: 9143 Sorted by residual: angle pdb=" N SER D 170 " pdb=" CA SER D 170 " pdb=" C SER D 170 " ideal model delta sigma weight residual 110.35 98.98 11.37 1.38e+00 5.25e-01 6.79e+01 angle pdb=" C GLU D 489 " pdb=" N PRO D 490 " pdb=" CA PRO D 490 " ideal model delta sigma weight residual 119.87 128.34 -8.47 1.04e+00 9.25e-01 6.63e+01 angle pdb=" C GLY A 526 " pdb=" N PRO A 527 " pdb=" CA PRO A 527 " ideal model delta sigma weight residual 119.85 127.88 -8.03 1.01e+00 9.80e-01 6.33e+01 angle pdb=" CB ASN D 90 " pdb=" CG ASN D 90 " pdb=" ND2 ASN D 90 " ideal model delta sigma weight residual 116.40 128.07 -11.67 1.50e+00 4.44e-01 6.05e+01 angle pdb=" N TYR A 380 " pdb=" CA TYR A 380 " pdb=" C TYR A 380 " ideal model delta sigma weight residual 114.31 104.49 9.82 1.29e+00 6.01e-01 5.80e+01 ... (remaining 9138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 3746 17.29 - 34.58: 134 34.58 - 51.88: 19 51.88 - 69.17: 12 69.17 - 86.46: 5 Dihedral angle restraints: 3916 sinusoidal: 1581 harmonic: 2335 Sorted by residual: dihedral pdb=" C TYR A 421 " pdb=" N TYR A 421 " pdb=" CA TYR A 421 " pdb=" CB TYR A 421 " ideal model delta harmonic sigma weight residual -122.60 -134.06 11.46 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" N TYR A 421 " pdb=" C TYR A 421 " pdb=" CA TYR A 421 " pdb=" CB TYR A 421 " ideal model delta harmonic sigma weight residual 122.80 133.46 -10.66 0 2.50e+00 1.60e-01 1.82e+01 dihedral pdb=" CA PRO D 389 " pdb=" C PRO D 389 " pdb=" N PHE D 390 " pdb=" CA PHE D 390 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 739 0.114 - 0.229: 209 0.229 - 0.343: 21 0.343 - 0.457: 7 0.457 - 0.572: 1 Chirality restraints: 977 Sorted by residual: chirality pdb=" CA TYR A 421 " pdb=" N TYR A 421 " pdb=" C TYR A 421 " pdb=" CB TYR A 421 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.17e+00 chirality pdb=" C1 NAG D1102 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG D1102 " pdb=" O5 NAG D1102 " both_signs ideal model delta sigma weight residual False -2.40 -2.84 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" C1 NAG D1104 " pdb=" ND2 ASN D 546 " pdb=" C2 NAG D1104 " pdb=" O5 NAG D1104 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 974 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 53 " 0.015 2.00e-02 2.50e+03 7.67e-02 7.35e+01 pdb=" CG ASN D 53 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN D 53 " -0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN D 53 " 0.125 2.00e-02 2.50e+03 pdb=" C1 NAG D1106 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 103 " -0.013 2.00e-02 2.50e+03 4.66e-02 2.71e+01 pdb=" CG ASN D 103 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN D 103 " 0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN D 103 " -0.075 2.00e-02 2.50e+03 pdb=" C1 NAG D1102 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 432 " -0.008 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" CG ASN D 432 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN D 432 " 0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN D 432 " -0.069 2.00e-02 2.50e+03 pdb=" C1 NAG D1103 " 0.048 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1264 2.76 - 3.29: 6404 3.29 - 3.83: 11299 3.83 - 4.36: 14413 4.36 - 4.90: 22737 Nonbonded interactions: 56117 Sorted by model distance: nonbonded pdb=" O4 NAG D1102 " pdb=" O6 NAG D1102 " model vdw 2.222 3.040 nonbonded pdb=" O4 NAG D1101 " pdb=" O6 NAG D1101 " model vdw 2.241 3.040 nonbonded pdb=" N SER D 170 " pdb=" O SER D 170 " model vdw 2.348 2.496 nonbonded pdb=" O4 NAG D1104 " pdb=" O6 NAG D1104 " model vdw 2.372 3.040 nonbonded pdb=" N TYR A 380 " pdb=" N GLY A 381 " model vdw 2.385 2.560 ... (remaining 56112 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: 8.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.160 Find NCS groups from input model: 0.010 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: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.018 0.135 6741 Z= 0.965 Angle : 1.707 12.716 9178 Z= 1.149 Chirality : 0.104 0.572 977 Planarity : 0.009 0.067 1177 Dihedral : 10.503 86.458 2397 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.89 % Favored : 97.98 % Rotamer: Outliers : 0.14 % Allowed : 1.00 % Favored : 98.86 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.28), residues: 792 helix: -0.42 (0.23), residues: 391 sheet: 0.78 (0.73), residues: 61 loop : 0.38 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 161 TYR 0.059 0.008 TYR D 199 PHE 0.028 0.006 PHE D 390 TRP 0.047 0.009 TRP D 349 HIS 0.014 0.003 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.01778 / 0.95 ( 6727) covalent geometry : angle 1.67848 / 1.15 ( 9143) SS BOND : bond 0.01568 / 1.02 ( 7) SS BOND : angle 2.49216 / 1.48 ( 14) hydrogen bonds : bond 0.17310 / 11.66 ( 322) hydrogen bonds : angle 7.10652 / 5.03 ( 909) link_NAG-ASN : bond 0.10760 / 5.86 ( 7) link_NAG-ASN : angle 6.52173 / 4.66 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ASN cc_start: 0.7073 (t0) cc_final: 0.6510 (m110) REVERT: A 418 ILE cc_start: 0.9251 (mm) cc_final: 0.8602 (mm) REVERT: D 119 ILE cc_start: 0.8517 (mt) cc_final: 0.8257 (mt) REVERT: D 155 SER cc_start: 0.8440 (t) cc_final: 0.8028 (p) REVERT: D 291 ILE cc_start: 0.8495 (pt) cc_final: 0.7995 (mp) REVERT: D 362 THR cc_start: 0.7357 (m) cc_final: 0.6891 (m) REVERT: D 441 LYS cc_start: 0.8694 (tttt) cc_final: 0.8471 (tptp) REVERT: D 474 MET cc_start: 0.8360 (mmp) cc_final: 0.8030 (mmm) REVERT: D 480 MET cc_start: 0.8661 (mtp) cc_final: 0.8432 (mtt) outliers start: 1 outliers final: 1 residues processed: 207 average time/residue: 0.0869 time to fit residues: 23.1462 Evaluate side-chains 117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN A 493 GLN A 498 GLN A 506 GLN D 154 ASN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** 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 = 0.3539 r_free = 0.3539 target = 0.094557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.083827 restraints weight = 18383.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.086257 restraints weight = 8663.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.087862 restraints weight = 5103.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.088883 restraints weight = 3471.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.089587 restraints weight = 2634.804| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6741 Z= 0.190 Angle : 0.844 20.805 9178 Z= 0.400 Chirality : 0.058 0.785 977 Planarity : 0.005 0.052 1177 Dihedral : 5.119 35.165 866 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.02 % Favored : 97.85 % Rotamer: Outliers : 1.86 % Allowed : 9.44 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.30), residues: 792 helix: 1.13 (0.26), residues: 390 sheet: 0.10 (0.72), residues: 61 loop : 0.36 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 219 TYR 0.017 0.002 TYR D 385 PHE 0.016 0.002 PHE D 369 TRP 0.022 0.002 TRP D 478 HIS 0.004 0.001 HIS D 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 ( 6727) covalent geometry : angle 0.71918 / 0.37 ( 9143) SS BOND : bond 0.00612 / 0.34 ( 7) SS BOND : angle 1.07647 / 0.77 ( 14) hydrogen bonds : bond 0.05981 / 4.01 ( 322) hydrogen bonds : angle 5.36780 / 3.79 ( 909) link_NAG-ASN : bond 0.01352 / 0.76 ( 7) link_NAG-ASN : angle 9.22631 / 6.41 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8765 (mm110) cc_final: 0.8554 (mt0) REVERT: A 462 LYS cc_start: 0.7833 (mppt) cc_final: 0.7476 (mppt) REVERT: D 206 ASP cc_start: 0.8561 (t0) cc_final: 0.8220 (t0) REVERT: D 270 MET cc_start: 0.7735 (tpp) cc_final: 0.7498 (tpp) REVERT: D 441 LYS cc_start: 0.8799 (tttt) cc_final: 0.8377 (tptp) REVERT: D 483 GLU cc_start: 0.8389 (tp30) cc_final: 0.7970 (tp30) outliers start: 13 outliers final: 8 residues processed: 149 average time/residue: 0.0685 time to fit residues: 13.6575 Evaluate side-chains 111 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 503 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS D 401 HIS D 417 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.092511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.081847 restraints weight = 18402.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.084223 restraints weight = 8736.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.085769 restraints weight = 5141.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.086742 restraints weight = 3510.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.087432 restraints weight = 2679.758| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6741 Z= 0.180 Angle : 0.771 21.054 9178 Z= 0.366 Chirality : 0.054 0.559 977 Planarity : 0.005 0.050 1177 Dihedral : 4.958 34.202 866 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.15 % Favored : 97.60 % Rotamer: Outliers : 2.72 % Allowed : 11.44 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.30), residues: 792 helix: 1.31 (0.26), residues: 393 sheet: -0.09 (0.69), residues: 60 loop : 0.29 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 466 TYR 0.019 0.001 TYR A 380 PHE 0.027 0.002 PHE D 327 TRP 0.027 0.002 TRP D 478 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 6727) covalent geometry : angle 0.66109 / 0.34 ( 9143) SS BOND : bond 0.00779 / 0.48 ( 7) SS BOND : angle 1.93266 / 1.68 ( 14) hydrogen bonds : bond 0.05317 / 3.57 ( 322) hydrogen bonds : angle 5.05729 / 3.56 ( 909) link_NAG-ASN : bond 0.01122 / 0.62 ( 7) link_NAG-ASN : angle 8.18064 / 6.03 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 206 ASP cc_start: 0.8576 (t0) cc_final: 0.7906 (t0) REVERT: D 270 MET cc_start: 0.7650 (tpp) cc_final: 0.7407 (tpp) REVERT: D 360 MET cc_start: 0.8023 (tmm) cc_final: 0.7639 (ttt) REVERT: D 406 GLU cc_start: 0.8384 (tp30) cc_final: 0.7761 (tp30) REVERT: D 441 LYS cc_start: 0.8884 (tttt) cc_final: 0.8425 (tptp) REVERT: D 479 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8232 (tm-30) REVERT: D 483 GLU cc_start: 0.8411 (tp30) cc_final: 0.8121 (tp30) REVERT: D 601 ASN cc_start: 0.8100 (t0) cc_final: 0.7865 (t0) outliers start: 19 outliers final: 15 residues processed: 125 average time/residue: 0.0801 time to fit residues: 13.5290 Evaluate side-chains 113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 210 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.092440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.081606 restraints weight = 18618.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083959 restraints weight = 8878.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.085488 restraints weight = 5243.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086486 restraints weight = 3599.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087152 restraints weight = 2749.446| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6741 Z= 0.157 Angle : 0.720 21.070 9178 Z= 0.340 Chirality : 0.051 0.461 977 Planarity : 0.004 0.050 1177 Dihedral : 4.750 33.384 866 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.27 % Favored : 97.60 % Rotamer: Outliers : 2.86 % Allowed : 13.02 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.30), residues: 792 helix: 1.40 (0.26), residues: 401 sheet: -0.35 (0.69), residues: 60 loop : 0.14 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 482 TYR 0.019 0.001 TYR A 380 PHE 0.027 0.002 PHE D 327 TRP 0.035 0.002 TRP D 478 HIS 0.003 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 6727) covalent geometry : angle 0.61392 / 0.32 ( 9143) SS BOND : bond 0.00547 / 0.36 ( 7) SS BOND : angle 1.59986 / 1.22 ( 14) hydrogen bonds : bond 0.04723 / 3.15 ( 322) hydrogen bonds : angle 4.84017 / 3.39 ( 909) link_NAG-ASN : bond 0.01160 / 0.64 ( 7) link_NAG-ASN : angle 7.79758 / 5.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.7929 (mppt) cc_final: 0.7587 (mppt) REVERT: D 190 MET cc_start: 0.8490 (tmm) cc_final: 0.8105 (tmm) REVERT: D 238 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8417 (mt-10) REVERT: D 259 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7856 (mp) REVERT: D 332 MET cc_start: 0.8243 (mmm) cc_final: 0.7940 (ttm) REVERT: D 360 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7175 (tmm) REVERT: D 375 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8056 (mm-30) REVERT: D 406 GLU cc_start: 0.8330 (tp30) cc_final: 0.7629 (tp30) REVERT: D 441 LYS cc_start: 0.8833 (tttt) cc_final: 0.8411 (tptp) REVERT: D 470 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7716 (mmtt) REVERT: D 479 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8163 (tm-30) REVERT: D 483 GLU cc_start: 0.8454 (tp30) cc_final: 0.8185 (tp30) REVERT: D 488 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7760 (m) outliers start: 20 outliers final: 13 residues processed: 125 average time/residue: 0.0780 time to fit residues: 12.9158 Evaluate side-chains 113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 0.0040 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.093153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.082156 restraints weight = 18813.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.084550 restraints weight = 8932.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086098 restraints weight = 5292.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.087100 restraints weight = 3640.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087815 restraints weight = 2788.649| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6741 Z= 0.136 Angle : 0.685 21.047 9178 Z= 0.323 Chirality : 0.051 0.427 977 Planarity : 0.004 0.050 1177 Dihedral : 4.598 32.489 866 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.40 % Favored : 97.47 % Rotamer: Outliers : 3.15 % Allowed : 14.31 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.30), residues: 792 helix: 1.51 (0.26), residues: 400 sheet: -0.39 (0.70), residues: 60 loop : 0.18 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 115 TYR 0.021 0.001 TYR D 497 PHE 0.026 0.002 PHE D 327 TRP 0.040 0.001 TRP D 478 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 6727) covalent geometry : angle 0.57922 / 0.30 ( 9143) SS BOND : bond 0.00576 / 0.36 ( 7) SS BOND : angle 1.32823 / 1.00 ( 14) hydrogen bonds : bond 0.04500 / 3.00 ( 322) hydrogen bonds : angle 4.68608 / 3.25 ( 909) link_NAG-ASN : bond 0.01182 / 0.65 ( 7) link_NAG-ASN : angle 7.58602 / 5.75 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.6435 (mmm) cc_final: 0.6139 (mmm) REVERT: D 190 MET cc_start: 0.8506 (tmm) cc_final: 0.8111 (tmm) REVERT: D 237 TYR cc_start: 0.9133 (t80) cc_final: 0.8918 (t80) REVERT: D 270 MET cc_start: 0.7827 (tpp) cc_final: 0.7584 (tpp) REVERT: D 285 PHE cc_start: 0.6380 (m-80) cc_final: 0.6143 (m-80) REVERT: D 323 MET cc_start: 0.9404 (tpp) cc_final: 0.9043 (mmm) REVERT: D 360 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6853 (tmm) REVERT: D 375 GLU cc_start: 0.8710 (mm-30) cc_final: 0.7971 (mm-30) REVERT: D 406 GLU cc_start: 0.8327 (tp30) cc_final: 0.7704 (tp30) REVERT: D 441 LYS cc_start: 0.8801 (tttt) cc_final: 0.8394 (tptp) REVERT: D 479 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8182 (tm-30) REVERT: D 483 GLU cc_start: 0.8482 (tp30) cc_final: 0.8231 (tp30) REVERT: D 488 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.7933 (m) REVERT: D 589 GLU cc_start: 0.7737 (tp30) cc_final: 0.7519 (tp30) outliers start: 22 outliers final: 18 residues processed: 125 average time/residue: 0.0739 time to fit residues: 12.5392 Evaluate side-chains 123 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079971 restraints weight = 18860.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.082291 restraints weight = 8990.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.083783 restraints weight = 5335.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.084785 restraints weight = 3678.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.085459 restraints weight = 2807.248| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6741 Z= 0.177 Angle : 0.710 21.117 9178 Z= 0.340 Chirality : 0.051 0.421 977 Planarity : 0.004 0.045 1177 Dihedral : 4.776 32.432 866 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.90 % Favored : 96.97 % Rotamer: Outliers : 3.58 % Allowed : 14.31 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.30), residues: 792 helix: 1.54 (0.26), residues: 397 sheet: -0.39 (0.71), residues: 60 loop : 0.18 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 454 TYR 0.018 0.002 TYR D 497 PHE 0.025 0.002 PHE D 327 TRP 0.038 0.002 TRP D 478 HIS 0.004 0.001 HIS D 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 6727) covalent geometry : angle 0.60796 / 0.32 ( 9143) SS BOND : bond 0.00507 / 0.31 ( 7) SS BOND : angle 1.30243 / 1.00 ( 14) hydrogen bonds : bond 0.04792 / 3.20 ( 322) hydrogen bonds : angle 4.72635 / 3.25 ( 909) link_NAG-ASN : bond 0.01110 / 0.61 ( 7) link_NAG-ASN : angle 7.65119 / 5.75 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.6713 (mmm) cc_final: 0.6299 (mmm) REVERT: D 190 MET cc_start: 0.8532 (tmm) cc_final: 0.8273 (tmm) REVERT: D 285 PHE cc_start: 0.6455 (m-80) cc_final: 0.6166 (m-80) REVERT: D 323 MET cc_start: 0.9407 (tpp) cc_final: 0.9119 (mmm) REVERT: D 375 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8002 (mm-30) REVERT: D 406 GLU cc_start: 0.8322 (tp30) cc_final: 0.7757 (tp30) REVERT: D 441 LYS cc_start: 0.8818 (tttt) cc_final: 0.8422 (tptp) REVERT: D 470 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7958 (tptt) REVERT: D 479 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8346 (tm-30) REVERT: D 480 MET cc_start: 0.8666 (mtt) cc_final: 0.8444 (mtt) outliers start: 25 outliers final: 17 residues processed: 119 average time/residue: 0.0797 time to fit residues: 12.5678 Evaluate side-chains 117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.080769 restraints weight = 18548.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083106 restraints weight = 8897.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084641 restraints weight = 5272.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085642 restraints weight = 3620.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.086315 restraints weight = 2764.738| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6741 Z= 0.164 Angle : 0.707 21.137 9178 Z= 0.338 Chirality : 0.051 0.410 977 Planarity : 0.004 0.046 1177 Dihedral : 4.705 31.978 866 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.53 % Favored : 97.35 % Rotamer: Outliers : 3.43 % Allowed : 15.02 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.30), residues: 792 helix: 1.59 (0.26), residues: 397 sheet: -0.29 (0.71), residues: 60 loop : 0.09 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 482 TYR 0.028 0.002 TYR D 158 PHE 0.027 0.002 PHE D 308 TRP 0.037 0.002 TRP D 478 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 6727) covalent geometry : angle 0.60618 / 0.32 ( 9143) SS BOND : bond 0.00598 / 0.37 ( 7) SS BOND : angle 1.21361 / 0.90 ( 14) hydrogen bonds : bond 0.04600 / 3.06 ( 322) hydrogen bonds : angle 4.68394 / 3.23 ( 909) link_NAG-ASN : bond 0.01112 / 0.61 ( 7) link_NAG-ASN : angle 7.58100 / 5.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 GLN cc_start: 0.8825 (mp10) cc_final: 0.8549 (mp10) REVERT: D 152 MET cc_start: 0.6785 (mmm) cc_final: 0.6428 (mmm) REVERT: D 190 MET cc_start: 0.8583 (tmm) cc_final: 0.8356 (tmm) REVERT: D 270 MET cc_start: 0.8095 (tpp) cc_final: 0.7854 (tpp) REVERT: D 285 PHE cc_start: 0.6492 (m-80) cc_final: 0.6221 (m-80) REVERT: D 323 MET cc_start: 0.9391 (tpp) cc_final: 0.9125 (mmm) REVERT: D 375 GLU cc_start: 0.8670 (mm-30) cc_final: 0.7965 (mm-30) REVERT: D 406 GLU cc_start: 0.8262 (tp30) cc_final: 0.7729 (tp30) REVERT: D 435 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7042 (mm-30) REVERT: D 441 LYS cc_start: 0.8800 (tttt) cc_final: 0.8409 (tptp) REVERT: D 470 LYS cc_start: 0.8218 (mmtt) cc_final: 0.8016 (tptt) REVERT: D 479 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8282 (tm-30) outliers start: 24 outliers final: 20 residues processed: 124 average time/residue: 0.0782 time to fit residues: 13.1922 Evaluate side-chains 120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.092216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081336 restraints weight = 18687.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083735 restraints weight = 8957.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085233 restraints weight = 5289.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.086283 restraints weight = 3654.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.086916 restraints weight = 2765.843| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6741 Z= 0.151 Angle : 0.766 21.121 9178 Z= 0.361 Chirality : 0.053 0.618 977 Planarity : 0.005 0.051 1177 Dihedral : 5.032 47.915 866 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.78 % Favored : 97.10 % Rotamer: Outliers : 3.15 % Allowed : 16.60 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.31), residues: 792 helix: 1.65 (0.26), residues: 397 sheet: -0.39 (0.72), residues: 60 loop : 0.11 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 482 TYR 0.026 0.002 TYR D 158 PHE 0.025 0.002 PHE D 327 TRP 0.027 0.001 TRP D 478 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 6727) covalent geometry : angle 0.65495 / 0.34 ( 9143) SS BOND : bond 0.00518 / 0.33 ( 7) SS BOND : angle 1.63663 / 0.95 ( 14) hydrogen bonds : bond 0.04486 / 2.97 ( 322) hydrogen bonds : angle 4.77381 / 3.24 ( 909) link_NAG-ASN : bond 0.01124 / 0.60 ( 7) link_NAG-ASN : angle 8.23993 / 6.57 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 GLN cc_start: 0.8810 (mp10) cc_final: 0.8533 (mp10) REVERT: D 152 MET cc_start: 0.6702 (mmm) cc_final: 0.6309 (mmm) REVERT: D 190 MET cc_start: 0.8551 (tmm) cc_final: 0.8312 (tmm) REVERT: D 270 MET cc_start: 0.8166 (tpp) cc_final: 0.7877 (tpp) REVERT: D 285 PHE cc_start: 0.6459 (m-80) cc_final: 0.6192 (m-80) REVERT: D 323 MET cc_start: 0.9404 (tpp) cc_final: 0.9143 (mmm) REVERT: D 375 GLU cc_start: 0.8704 (mm-30) cc_final: 0.7929 (mm-30) REVERT: D 406 GLU cc_start: 0.8255 (tp30) cc_final: 0.7717 (tp30) REVERT: D 441 LYS cc_start: 0.8805 (tttt) cc_final: 0.8306 (tptp) REVERT: D 479 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8083 (tm-30) outliers start: 22 outliers final: 18 residues processed: 118 average time/residue: 0.0686 time to fit residues: 11.3289 Evaluate side-chains 118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.0270 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN D 61 ASN ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.092463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.081597 restraints weight = 18940.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.083983 restraints weight = 8981.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085522 restraints weight = 5284.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086557 restraints weight = 3620.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087229 restraints weight = 2737.419| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6741 Z= 0.150 Angle : 0.712 21.068 9178 Z= 0.343 Chirality : 0.048 0.396 977 Planarity : 0.004 0.043 1177 Dihedral : 4.799 37.138 866 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.65 % Favored : 97.22 % Rotamer: Outliers : 2.86 % Allowed : 16.74 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.31), residues: 792 helix: 1.72 (0.26), residues: 397 sheet: 0.25 (0.80), residues: 50 loop : 0.06 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 482 TYR 0.025 0.001 TYR D 158 PHE 0.024 0.001 PHE D 327 TRP 0.023 0.001 TRP D 473 HIS 0.003 0.001 HIS D 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 6727) covalent geometry : angle 0.62237 / 0.32 ( 9143) SS BOND : bond 0.00524 / 0.34 ( 7) SS BOND : angle 1.51167 / 0.89 ( 14) hydrogen bonds : bond 0.04381 / 2.92 ( 322) hydrogen bonds : angle 4.76831 / 3.23 ( 909) link_NAG-ASN : bond 0.01091 / 0.57 ( 7) link_NAG-ASN : angle 7.18613 / 5.54 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8366 (pttt) cc_final: 0.8093 (ptpp) REVERT: D 35 GLN cc_start: 0.8818 (mp10) cc_final: 0.8520 (mp10) REVERT: D 152 MET cc_start: 0.6671 (mmm) cc_final: 0.6242 (mmm) REVERT: D 190 MET cc_start: 0.8472 (tmm) cc_final: 0.8113 (tmm) REVERT: D 237 TYR cc_start: 0.9133 (t80) cc_final: 0.8899 (t80) REVERT: D 270 MET cc_start: 0.8184 (tpp) cc_final: 0.7878 (tpp) REVERT: D 323 MET cc_start: 0.9428 (tpp) cc_final: 0.9025 (mmm) REVERT: D 376 MET cc_start: 0.9065 (ttm) cc_final: 0.8822 (ttm) REVERT: D 439 LEU cc_start: 0.8767 (mt) cc_final: 0.8472 (mt) REVERT: D 441 LYS cc_start: 0.8831 (tttt) cc_final: 0.8295 (tptp) REVERT: D 479 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8020 (tm-30) outliers start: 20 outliers final: 16 residues processed: 116 average time/residue: 0.0750 time to fit residues: 11.9875 Evaluate side-chains 112 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 5 optimal weight: 0.0060 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 0.0020 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.094148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.083333 restraints weight = 18547.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.085745 restraints weight = 8822.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087311 restraints weight = 5191.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.088332 restraints weight = 3533.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088991 restraints weight = 2672.608| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6741 Z= 0.132 Angle : 0.692 20.971 9178 Z= 0.333 Chirality : 0.047 0.387 977 Planarity : 0.005 0.049 1177 Dihedral : 4.598 30.684 866 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.78 % Favored : 97.10 % Rotamer: Outliers : 2.15 % Allowed : 17.45 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.31), residues: 792 helix: 1.80 (0.26), residues: 397 sheet: 0.25 (0.81), residues: 50 loop : 0.06 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 482 TYR 0.025 0.002 TYR D 158 PHE 0.023 0.001 PHE D 327 TRP 0.025 0.001 TRP D 473 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6727) covalent geometry : angle 0.60230 / 0.31 ( 9143) SS BOND : bond 0.00559 / 0.37 ( 7) SS BOND : angle 1.43457 / 0.83 ( 14) hydrogen bonds : bond 0.04160 / 2.76 ( 322) hydrogen bonds : angle 4.71184 / 3.19 ( 909) link_NAG-ASN : bond 0.01103 / 0.57 ( 7) link_NAG-ASN : angle 7.07945 / 5.48 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8316 (pttt) cc_final: 0.8086 (ptpp) REVERT: D 35 GLN cc_start: 0.8795 (mp10) cc_final: 0.8526 (mp10) REVERT: D 152 MET cc_start: 0.6701 (mmm) cc_final: 0.6380 (mmm) REVERT: D 190 MET cc_start: 0.8519 (tmm) cc_final: 0.8104 (tmm) REVERT: D 237 TYR cc_start: 0.9151 (t80) cc_final: 0.8923 (t80) REVERT: D 249 MET cc_start: 0.7140 (mmm) cc_final: 0.6839 (mmm) REVERT: D 270 MET cc_start: 0.8187 (tpp) cc_final: 0.7919 (tpp) REVERT: D 323 MET cc_start: 0.9448 (tpp) cc_final: 0.8935 (mmm) REVERT: D 375 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8008 (mm-30) REVERT: D 376 MET cc_start: 0.9078 (ttm) cc_final: 0.8834 (ttm) REVERT: D 439 LEU cc_start: 0.8788 (mt) cc_final: 0.8468 (mt) REVERT: D 441 LYS cc_start: 0.8799 (tttt) cc_final: 0.8320 (tptp) REVERT: D 479 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8085 (tm-30) outliers start: 15 outliers final: 13 residues processed: 118 average time/residue: 0.0774 time to fit residues: 12.5258 Evaluate side-chains 115 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081240 restraints weight = 18608.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083587 restraints weight = 8893.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085131 restraints weight = 5256.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.086119 restraints weight = 3582.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.086778 restraints weight = 2726.511| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6741 Z= 0.177 Angle : 0.731 20.996 9178 Z= 0.356 Chirality : 0.049 0.397 977 Planarity : 0.005 0.047 1177 Dihedral : 4.794 29.993 866 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.90 % Favored : 96.97 % Rotamer: Outliers : 2.00 % Allowed : 18.17 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.31), residues: 792 helix: 1.73 (0.26), residues: 397 sheet: -0.36 (0.72), residues: 60 loop : 0.04 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 482 TYR 0.025 0.002 TYR D 158 PHE 0.031 0.002 PHE D 327 TRP 0.029 0.001 TRP D 473 HIS 0.005 0.001 HIS D 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 ( 6727) covalent geometry : angle 0.64566 / 0.34 ( 9143) SS BOND : bond 0.00600 / 0.37 ( 7) SS BOND : angle 1.64087 / 0.98 ( 14) hydrogen bonds : bond 0.04526 / 3.01 ( 322) hydrogen bonds : angle 4.83611 / 3.29 ( 909) link_NAG-ASN : bond 0.01031 / 0.53 ( 7) link_NAG-ASN : angle 7.09626 / 5.44 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1376.15 seconds wall clock time: 24 minutes 29.43 seconds (1469.43 seconds total)