Starting phenix.real_space_refine on Thu Jul 2 04:26:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dv1_27730/07_2026/8dv1_27730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dv1_27730/07_2026/8dv1_27730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dv1_27730/07_2026/8dv1_27730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dv1_27730/07_2026/8dv1_27730.map" model { file = "/net/cci-nas-00/data/ceres_data/8dv1_27730/07_2026/8dv1_27730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dv1_27730/07_2026/8dv1_27730.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dv1_27730/07_2026/8dv1_27730.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dv1_27730/07_2026/8dv1_27730.cif" } resolution = 3.4 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= 0.038 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 4183 2.51 5 N 1074 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 6543 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: 4855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4855 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: 1.43, per 1000 atoms: 0.22 Number of scatterers: 6543 At special positions: 0 Unit cell: (76.311, 87.57, 126.351, 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 1249 8.00 N 1074 7.00 C 4183 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 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=2.03 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 D1001 " - " ASN D 322 " " NAG D1002 " - " ASN D 103 " " NAG D1003 " - " ASN D 432 " " NAG D1004 " - " ASN D 546 " " NAG D1005 " - " ASN D 90 " " NAG D1006 " - " ASN D 53 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 350.4 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: 43 helices and 6 sheets defined 58.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.677A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.589A 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: 4.108A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.969A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 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 137 through 141 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.736A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 4.486A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (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 220 through 252 Proline residue: D 235 - end of helix removed outlier: 3.996A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) 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 317 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 413 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 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 485 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: 4.078A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.881A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 Proline residue: D 590 - end of helix 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: 6.915A 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 262 through 263 removed outlier: 6.072A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 350 323 hydrogen bonds defined for protein. 906 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: 0.85 Time building geometry restraints manager: 0.80 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: 1266 1.32 - 1.45: 2072 1.45 - 1.58: 3320 1.58 - 1.71: 9 1.71 - 1.84: 58 Bond restraints: 6725 Sorted by residual: bond pdb=" CD2 TRP D 477 " pdb=" CE3 TRP D 477 " ideal model delta sigma weight residual 1.398 1.306 0.092 1.60e-02 3.91e+03 3.28e+01 bond pdb=" CB SER D 44 " pdb=" OG SER D 44 " ideal model delta sigma weight residual 1.417 1.313 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CB TYR A 421 " pdb=" CG TYR A 421 " ideal model delta sigma weight residual 1.512 1.402 0.110 2.20e-02 2.07e+03 2.48e+01 bond pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 1.516 1.392 0.124 2.50e-02 1.60e+03 2.45e+01 bond pdb=" CB HIS D 540 " pdb=" CG HIS D 540 " ideal model delta sigma weight residual 1.497 1.430 0.067 1.40e-02 5.10e+03 2.29e+01 ... (remaining 6720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 7553 2.16 - 4.32: 1363 4.32 - 6.47: 181 6.47 - 8.63: 35 8.63 - 10.79: 8 Bond angle restraints: 9140 Sorted by residual: angle pdb=" C GLY D 537 " pdb=" N PRO D 538 " pdb=" CA PRO D 538 " ideal model delta sigma weight residual 119.78 128.55 -8.77 1.03e+00 9.43e-01 7.24e+01 angle pdb=" C ALA A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.47 129.12 -9.65 1.16e+00 7.43e-01 6.93e+01 angle pdb=" C ASN D 137 " pdb=" N PRO D 138 " pdb=" CA PRO D 138 " ideal model delta sigma weight residual 119.56 127.64 -8.08 1.02e+00 9.61e-01 6.28e+01 angle pdb=" C VAL D 283 " pdb=" N PRO D 284 " pdb=" CA PRO D 284 " ideal model delta sigma weight residual 119.24 127.24 -8.00 1.04e+00 9.25e-01 5.91e+01 angle pdb=" C SER D 611 " pdb=" N PRO D 612 " pdb=" CA PRO D 612 " ideal model delta sigma weight residual 119.82 127.13 -7.31 9.80e-01 1.04e+00 5.57e+01 ... (remaining 9135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3737 17.80 - 35.59: 139 35.59 - 53.39: 22 53.39 - 71.19: 12 71.19 - 88.98: 5 Dihedral angle restraints: 3915 sinusoidal: 1580 harmonic: 2335 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -140.80 54.80 1 1.00e+01 1.00e-02 4.07e+01 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 -135.05 12.45 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CA ALA D 153 " pdb=" C ALA D 153 " pdb=" N ASN D 154 " pdb=" CA ASN D 154 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 3912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 838 0.137 - 0.274: 124 0.274 - 0.412: 10 0.412 - 0.549: 3 0.549 - 0.686: 1 Chirality restraints: 976 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 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.93 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" C2 NAG D1002 " pdb=" C1 NAG D1002 " pdb=" C3 NAG D1002 " pdb=" N2 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.49 -3.00 0.50 2.00e-01 2.50e+01 6.35e+00 ... (remaining 973 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 90 " 0.217 2.00e-02 2.50e+03 2.54e-01 8.05e+02 pdb=" CG ASN D 90 " -0.123 2.00e-02 2.50e+03 pdb=" OD1 ASN D 90 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN D 90 " -0.403 2.00e-02 2.50e+03 pdb=" C1 NAG D1005 " 0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 163 " 0.287 2.00e-02 2.50e+03 1.39e-01 4.80e+02 pdb=" CG TRP D 163 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP D 163 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP D 163 " -0.148 2.00e-02 2.50e+03 pdb=" NE1 TRP D 163 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TRP D 163 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP D 163 " -0.174 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 163 " 0.148 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 163 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP D 163 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.135 2.00e-02 2.50e+03 1.44e-01 2.59e+02 pdb=" CG ASN A 343 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.171 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1716 2.80 - 3.33: 6477 3.33 - 3.85: 11592 3.85 - 4.38: 14234 4.38 - 4.90: 22417 Nonbonded interactions: 56436 Sorted by model distance: nonbonded pdb=" O4 NAG D1004 " pdb=" O6 NAG D1004 " model vdw 2.277 3.040 nonbonded pdb=" N ASN D 103 " pdb=" OD1 ASN D 103 " model vdw 2.318 3.120 nonbonded pdb=" N ASN D 432 " pdb=" OD1 ASN D 432 " model vdw 2.327 3.120 nonbonded pdb=" N ASN D 546 " pdb=" OD1 ASN D 546 " model vdw 2.356 3.120 nonbonded pdb=" N ASN D 322 " pdb=" OD1 ASN D 322 " model vdw 2.411 3.120 ... (remaining 56431 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 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: 5.400 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.090 Find NCS groups from input model: 0.020 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:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 0.125 6739 Z= 0.970 Angle : 1.726 12.104 9175 Z= 1.170 Chirality : 0.101 0.686 976 Planarity : 0.011 0.139 1177 Dihedral : 10.823 88.982 2396 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.43 % Allowed : 1.57 % Favored : 98.00 % Cbeta Deviations : 0.27 % 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: -0.24 (0.28), residues: 792 helix: -0.33 (0.23), residues: 378 sheet: 0.33 (0.67), residues: 58 loop : 0.18 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 177 TYR 0.070 0.011 TYR D 180 PHE 0.069 0.008 PHE D 32 TRP 0.287 0.015 TRP D 163 HIS 0.010 0.002 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.01796 / 0.96 ( 6725) covalent geometry : angle 1.70873 / 1.17 ( 9140) SS BOND : bond 0.00792 / 0.44 ( 7) SS BOND : angle 1.59109 / 0.97 ( 14) hydrogen bonds : bond 0.17554 / 11.31 ( 323) hydrogen bonds : angle 7.51538 / 5.25 ( 906) link_NAG-ASN : bond 0.08250 / 4.55 ( 7) link_NAG-ASN : angle 5.45673 / 3.95 ( 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 201 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 198 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.7661 (m-40) cc_final: 0.7098 (p0) REVERT: A 472 ILE cc_start: 0.7249 (mm) cc_final: 0.7040 (mm) REVERT: A 500 THR cc_start: 0.8413 (p) cc_final: 0.8103 (p) REVERT: D 476 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8347 (mptt) outliers start: 3 outliers final: 1 residues processed: 200 average time/residue: 0.0808 time to fit residues: 20.7225 Evaluate side-chains 119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 322 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 61 ASN D 96 GLN D 401 HIS D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.098379 restraints weight = 15179.266| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.01 r_work: 0.3335 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6739 Z= 0.178 Angle : 0.767 19.998 9175 Z= 0.372 Chirality : 0.054 0.644 976 Planarity : 0.005 0.041 1177 Dihedral : 4.971 20.841 866 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.72 % Allowed : 9.59 % 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: 1.09 (0.30), residues: 792 helix: 1.29 (0.27), residues: 375 sheet: 0.02 (0.66), residues: 60 loop : 0.39 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 466 TYR 0.022 0.002 TYR D 183 PHE 0.018 0.002 PHE D 369 TRP 0.017 0.002 TRP D 163 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 6725) covalent geometry : angle 0.67935 / 0.35 ( 9140) SS BOND : bond 0.00490 / 0.22 ( 7) SS BOND : angle 1.61469 / 0.81 ( 14) hydrogen bonds : bond 0.05193 / 3.35 ( 323) hydrogen bonds : angle 5.40003 / 3.75 ( 906) link_NAG-ASN : bond 0.00918 / 0.49 ( 7) link_NAG-ASN : angle 7.39019 / 5.23 ( 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 164 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7867 (pt) cc_final: 0.7383 (pt) REVERT: A 355 ARG cc_start: 0.8697 (tpt170) cc_final: 0.8269 (tpt170) REVERT: A 469 SER cc_start: 0.8727 (t) cc_final: 0.8372 (p) REVERT: A 523 THR cc_start: 0.8050 (m) cc_final: 0.7753 (p) REVERT: D 26 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8297 (ttmt) REVERT: D 56 GLU cc_start: 0.8145 (pm20) cc_final: 0.7680 (pm20) REVERT: D 60 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8226 (mm-40) REVERT: D 115 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.7930 (mmm-85) REVERT: D 168 TRP cc_start: 0.6893 (t-100) cc_final: 0.6352 (t-100) REVERT: D 174 LYS cc_start: 0.8271 (ttmt) cc_final: 0.8051 (ttmm) REVERT: D 206 ASP cc_start: 0.9122 (t70) cc_final: 0.8697 (t0) REVERT: D 210 ASN cc_start: 0.7693 (m-40) cc_final: 0.7424 (m110) REVERT: D 249 MET cc_start: 0.7888 (tpt) cc_final: 0.7672 (tpt) REVERT: D 270 MET cc_start: 0.7633 (mmt) cc_final: 0.7378 (tpp) REVERT: D 447 VAL cc_start: 0.9018 (t) cc_final: 0.8710 (p) REVERT: D 472 GLN cc_start: 0.7189 (mt0) cc_final: 0.6659 (mp10) REVERT: D 476 LYS cc_start: 0.8353 (mmmt) cc_final: 0.8069 (tptt) REVERT: D 577 LYS cc_start: 0.7441 (mttt) cc_final: 0.7166 (mtpt) outliers start: 12 outliers final: 5 residues processed: 157 average time/residue: 0.0746 time to fit residues: 15.5198 Evaluate side-chains 129 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 233 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.0270 chunk 32 optimal weight: 2.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN D 61 ASN D 373 HIS D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.108430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.095139 restraints weight = 15200.173| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.99 r_work: 0.3289 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6739 Z= 0.186 Angle : 0.757 19.340 9175 Z= 0.358 Chirality : 0.052 0.579 976 Planarity : 0.004 0.029 1177 Dihedral : 4.727 17.135 864 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.00 % Allowed : 9.73 % Favored : 87.27 % 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: 1.36 (0.27), residues: 379 sheet: -0.43 (0.65), residues: 61 loop : 0.21 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 582 TYR 0.019 0.001 TYR D 385 PHE 0.020 0.002 PHE A 374 TRP 0.014 0.002 TRP D 478 HIS 0.007 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 ( 6725) covalent geometry : angle 0.66857 / 0.34 ( 9140) SS BOND : bond 0.00606 / 0.17 ( 7) SS BOND : angle 1.72817 / 0.80 ( 14) hydrogen bonds : bond 0.05153 / 3.31 ( 323) hydrogen bonds : angle 5.06078 / 3.51 ( 906) link_NAG-ASN : bond 0.00935 / 0.58 ( 7) link_NAG-ASN : angle 7.34240 / 5.21 ( 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 147 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.169 Fit side-chains REVERT: A 386 LYS cc_start: 0.8754 (mtmm) cc_final: 0.8543 (pttm) REVERT: A 469 SER cc_start: 0.8693 (t) cc_final: 0.8398 (p) REVERT: A 498 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: D 26 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8538 (ttmt) REVERT: D 56 GLU cc_start: 0.8168 (pm20) cc_final: 0.7690 (pm20) REVERT: D 60 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8280 (mm-40) REVERT: D 63 ASN cc_start: 0.8451 (m-40) cc_final: 0.7947 (m-40) REVERT: D 115 ARG cc_start: 0.8442 (mmm-85) cc_final: 0.8216 (mmm-85) REVERT: D 168 TRP cc_start: 0.6883 (t-100) cc_final: 0.6190 (t-100) REVERT: D 206 ASP cc_start: 0.9089 (t70) cc_final: 0.8744 (t0) REVERT: D 210 ASN cc_start: 0.7855 (m-40) cc_final: 0.7583 (m-40) REVERT: D 401 HIS cc_start: 0.8741 (OUTLIER) cc_final: 0.7661 (t-90) REVERT: D 472 GLN cc_start: 0.7278 (mt0) cc_final: 0.6732 (mp10) REVERT: D 476 LYS cc_start: 0.8084 (mmmt) cc_final: 0.7848 (tppt) REVERT: D 494 ASP cc_start: 0.8732 (t70) cc_final: 0.8398 (t0) outliers start: 21 outliers final: 10 residues processed: 138 average time/residue: 0.0836 time to fit residues: 15.3515 Evaluate side-chains 129 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.108632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.095926 restraints weight = 15626.708| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.77 r_work: 0.3346 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6739 Z= 0.188 Angle : 0.726 19.830 9175 Z= 0.342 Chirality : 0.051 0.586 976 Planarity : 0.004 0.027 1177 Dihedral : 4.623 18.614 864 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.72 % Allowed : 11.59 % Favored : 85.69 % 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: 0.90 (0.30), residues: 792 helix: 1.33 (0.26), residues: 380 sheet: -0.51 (0.64), residues: 61 loop : 0.12 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 466 TYR 0.018 0.001 TYR D 385 PHE 0.013 0.002 PHE D 230 TRP 0.012 0.001 TRP D 165 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 ( 6725) covalent geometry : angle 0.63097 / 0.32 ( 9140) SS BOND : bond 0.00434 / 0.14 ( 7) SS BOND : angle 1.96921 / 0.89 ( 14) hydrogen bonds : bond 0.04839 / 3.10 ( 323) hydrogen bonds : angle 4.93548 / 3.42 ( 906) link_NAG-ASN : bond 0.00894 / 0.58 ( 7) link_NAG-ASN : angle 7.35718 / 5.25 ( 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 144 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.249 Fit side-chains REVERT: A 469 SER cc_start: 0.8595 (t) cc_final: 0.8300 (p) REVERT: A 498 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: D 56 GLU cc_start: 0.8169 (pm20) cc_final: 0.7626 (pm20) REVERT: D 63 ASN cc_start: 0.8501 (m-40) cc_final: 0.8105 (m-40) REVERT: D 115 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.7981 (mmm160) REVERT: D 174 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8073 (mttp) REVERT: D 206 ASP cc_start: 0.9021 (t70) cc_final: 0.8751 (t0) REVERT: D 401 HIS cc_start: 0.8698 (OUTLIER) cc_final: 0.7691 (t-90) outliers start: 19 outliers final: 11 residues processed: 135 average time/residue: 0.0713 time to fit residues: 12.8580 Evaluate side-chains 131 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.108827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.096258 restraints weight = 15639.332| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.76 r_work: 0.3350 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6739 Z= 0.165 Angle : 0.722 19.924 9175 Z= 0.334 Chirality : 0.050 0.571 976 Planarity : 0.003 0.027 1177 Dihedral : 4.499 17.954 864 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.72 % Allowed : 13.02 % Favored : 84.26 % 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: 0.94 (0.30), residues: 792 helix: 1.44 (0.26), residues: 381 sheet: -0.67 (0.62), residues: 61 loop : 0.07 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 408 TYR 0.017 0.001 TYR D 385 PHE 0.012 0.001 PHE D 230 TRP 0.011 0.001 TRP D 165 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 6725) covalent geometry : angle 0.63044 / 0.31 ( 9140) SS BOND : bond 0.00379 / 0.12 ( 7) SS BOND : angle 1.59072 / 0.72 ( 14) hydrogen bonds : bond 0.04632 / 2.97 ( 323) hydrogen bonds : angle 4.88888 / 3.37 ( 906) link_NAG-ASN : bond 0.00895 / 0.58 ( 7) link_NAG-ASN : angle 7.28565 / 5.21 ( 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 143 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.165 Fit side-chains REVERT: A 469 SER cc_start: 0.8666 (t) cc_final: 0.8372 (p) REVERT: A 498 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: D 56 GLU cc_start: 0.8113 (pm20) cc_final: 0.7680 (pm20) REVERT: D 63 ASN cc_start: 0.8471 (m-40) cc_final: 0.8078 (m-40) REVERT: D 115 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.8009 (mmm160) REVERT: D 206 ASP cc_start: 0.9025 (t70) cc_final: 0.8770 (t0) REVERT: D 401 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.7633 (t-90) outliers start: 19 outliers final: 14 residues processed: 132 average time/residue: 0.0855 time to fit residues: 14.9177 Evaluate side-chains 130 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 530 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.0070 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.110689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098025 restraints weight = 15588.747| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.78 r_work: 0.3382 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6739 Z= 0.131 Angle : 0.692 19.623 9175 Z= 0.318 Chirality : 0.048 0.523 976 Planarity : 0.003 0.027 1177 Dihedral : 4.300 17.336 864 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.72 % Allowed : 13.02 % Favored : 84.26 % 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: 1.03 (0.31), residues: 792 helix: 1.54 (0.27), residues: 381 sheet: -0.62 (0.64), residues: 61 loop : 0.08 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 582 TYR 0.018 0.001 TYR D 385 PHE 0.012 0.001 PHE D 369 TRP 0.012 0.001 TRP D 165 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 6725) covalent geometry : angle 0.60511 / 0.30 ( 9140) SS BOND : bond 0.00276 / 0.12 ( 7) SS BOND : angle 1.33399 / 0.61 ( 14) hydrogen bonds : bond 0.04231 / 2.73 ( 323) hydrogen bonds : angle 4.78724 / 3.27 ( 906) link_NAG-ASN : bond 0.00978 / 0.63 ( 7) link_NAG-ASN : angle 6.95878 / 4.97 ( 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 136 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.249 Fit side-chains REVERT: A 364 ASP cc_start: 0.6738 (t70) cc_final: 0.5843 (m-30) REVERT: A 469 SER cc_start: 0.8636 (t) cc_final: 0.8351 (p) REVERT: A 498 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: D 56 GLU cc_start: 0.8057 (pm20) cc_final: 0.7682 (pm20) REVERT: D 63 ASN cc_start: 0.8472 (m-40) cc_final: 0.8115 (m-40) REVERT: D 249 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7306 (tpp) REVERT: D 494 ASP cc_start: 0.8531 (t70) cc_final: 0.8307 (t70) outliers start: 19 outliers final: 12 residues processed: 127 average time/residue: 0.0810 time to fit residues: 13.8431 Evaluate side-chains 120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 0.0670 chunk 56 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.109264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.096880 restraints weight = 15469.448| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.73 r_work: 0.3363 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6739 Z= 0.157 Angle : 0.695 19.738 9175 Z= 0.325 Chirality : 0.049 0.550 976 Planarity : 0.003 0.027 1177 Dihedral : 4.361 17.903 864 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.58 % Allowed : 13.73 % Favored : 83.69 % 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 (0.31), residues: 792 helix: 1.52 (0.26), residues: 380 sheet: -0.61 (0.65), residues: 61 loop : 0.03 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 115 TYR 0.018 0.001 TYR D 385 PHE 0.012 0.001 PHE D 369 TRP 0.013 0.001 TRP D 168 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 6725) covalent geometry : angle 0.60814 / 0.31 ( 9140) SS BOND : bond 0.00210 / 0.09 ( 7) SS BOND : angle 1.37252 / 0.68 ( 14) hydrogen bonds : bond 0.04415 / 2.83 ( 323) hydrogen bonds : angle 4.84805 / 3.32 ( 906) link_NAG-ASN : bond 0.00928 / 0.61 ( 7) link_NAG-ASN : angle 7.00014 / 5.00 ( 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: 18 poor density : 116 time to evaluate : 0.248 Fit side-chains REVERT: A 469 SER cc_start: 0.8664 (t) cc_final: 0.8354 (p) REVERT: A 498 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7830 (mt0) REVERT: D 63 ASN cc_start: 0.8573 (m-40) cc_final: 0.8220 (m-40) REVERT: D 115 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7857 (mmm-85) REVERT: D 249 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7377 (tpp) REVERT: D 310 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7883 (mm-30) outliers start: 18 outliers final: 14 residues processed: 126 average time/residue: 0.0782 time to fit residues: 13.3777 Evaluate side-chains 123 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 46 optimal weight: 0.0050 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.109776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097261 restraints weight = 15607.029| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.76 r_work: 0.3374 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6739 Z= 0.147 Angle : 0.706 19.820 9175 Z= 0.326 Chirality : 0.049 0.537 976 Planarity : 0.003 0.027 1177 Dihedral : 4.346 17.566 864 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.29 % Allowed : 14.45 % Favored : 83.26 % 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: 0.94 (0.31), residues: 792 helix: 1.41 (0.26), residues: 388 sheet: -0.51 (0.65), residues: 60 loop : 0.06 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 115 TYR 0.018 0.001 TYR D 385 PHE 0.011 0.001 PHE D 230 TRP 0.011 0.001 TRP D 165 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6725) covalent geometry : angle 0.61985 / 0.31 ( 9140) SS BOND : bond 0.00205 / 0.11 ( 7) SS BOND : angle 1.41609 / 0.73 ( 14) hydrogen bonds : bond 0.04317 / 2.77 ( 323) hydrogen bonds : angle 4.82913 / 3.29 ( 906) link_NAG-ASN : bond 0.00924 / 0.61 ( 7) link_NAG-ASN : angle 6.99723 / 5.00 ( 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 128 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.198 Fit side-chains REVERT: A 469 SER cc_start: 0.8651 (t) cc_final: 0.8347 (p) REVERT: A 498 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7811 (mt0) REVERT: D 63 ASN cc_start: 0.8549 (m-40) cc_final: 0.8292 (m-40) REVERT: D 115 ARG cc_start: 0.8204 (mmm160) cc_final: 0.7914 (mmm-85) REVERT: D 249 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7346 (tpp) REVERT: D 310 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7764 (mm-30) REVERT: D 530 CYS cc_start: 0.7320 (t) cc_final: 0.7071 (t) outliers start: 16 outliers final: 14 residues processed: 119 average time/residue: 0.0822 time to fit residues: 13.2196 Evaluate side-chains 125 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.0060 chunk 1 optimal weight: 0.4980 chunk 19 optimal weight: 0.0270 chunk 70 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.110864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.098371 restraints weight = 15745.351| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.78 r_work: 0.3394 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6739 Z= 0.133 Angle : 0.687 19.619 9175 Z= 0.320 Chirality : 0.048 0.515 976 Planarity : 0.003 0.027 1177 Dihedral : 4.255 17.251 864 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.43 % Allowed : 14.59 % Favored : 82.98 % 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: 1.01 (0.31), residues: 792 helix: 1.48 (0.27), residues: 385 sheet: -0.50 (0.66), residues: 60 loop : 0.08 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 115 TYR 0.018 0.001 TYR D 385 PHE 0.014 0.001 PHE A 374 TRP 0.012 0.001 TRP D 477 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 6725) covalent geometry : angle 0.60665 / 0.30 ( 9140) SS BOND : bond 0.00323 / 0.15 ( 7) SS BOND : angle 1.26367 / 0.64 ( 14) hydrogen bonds : bond 0.04122 / 2.65 ( 323) hydrogen bonds : angle 4.79482 / 3.26 ( 906) link_NAG-ASN : bond 0.00968 / 0.63 ( 7) link_NAG-ASN : angle 6.68337 / 4.76 ( 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 132 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.182 Fit side-chains REVERT: A 469 SER cc_start: 0.8641 (t) cc_final: 0.8338 (p) REVERT: A 498 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: D 56 GLU cc_start: 0.8028 (pm20) cc_final: 0.7773 (pm20) REVERT: D 63 ASN cc_start: 0.8472 (m-40) cc_final: 0.8155 (m-40) REVERT: D 189 GLU cc_start: 0.8258 (tp30) cc_final: 0.8010 (tp30) REVERT: D 249 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7322 (tpp) REVERT: D 290 ASN cc_start: 0.7698 (t0) cc_final: 0.7431 (t0) REVERT: D 530 CYS cc_start: 0.7382 (t) cc_final: 0.7141 (t) outliers start: 17 outliers final: 14 residues processed: 125 average time/residue: 0.0818 time to fit residues: 13.5249 Evaluate side-chains 122 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 15 optimal weight: 0.0010 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.111592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.098998 restraints weight = 15543.656| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.77 r_work: 0.3404 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6739 Z= 0.132 Angle : 0.683 19.606 9175 Z= 0.323 Chirality : 0.048 0.516 976 Planarity : 0.003 0.027 1177 Dihedral : 4.298 17.696 864 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.58 % Allowed : 15.45 % Favored : 81.97 % 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: 0.99 (0.31), residues: 792 helix: 1.40 (0.26), residues: 386 sheet: -0.51 (0.68), residues: 60 loop : 0.16 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 582 TYR 0.018 0.001 TYR D 385 PHE 0.012 0.001 PHE D 369 TRP 0.014 0.001 TRP D 477 HIS 0.003 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 6725) covalent geometry : angle 0.60615 / 0.30 ( 9140) SS BOND : bond 0.00309 / 0.15 ( 7) SS BOND : angle 1.20952 / 0.62 ( 14) hydrogen bonds : bond 0.04190 / 2.70 ( 323) hydrogen bonds : angle 4.86096 / 3.32 ( 906) link_NAG-ASN : bond 0.00987 / 0.64 ( 7) link_NAG-ASN : angle 6.56092 / 4.66 ( 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 130 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.196 Fit side-chains REVERT: A 469 SER cc_start: 0.8543 (t) cc_final: 0.8307 (p) REVERT: A 498 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7794 (mt0) REVERT: D 63 ASN cc_start: 0.8459 (m-40) cc_final: 0.8175 (m-40) REVERT: D 134 ASN cc_start: 0.2117 (t0) cc_final: 0.1687 (t0) REVERT: D 249 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7334 (tpp) REVERT: D 290 ASN cc_start: 0.7684 (t0) cc_final: 0.7367 (t0) REVERT: D 530 CYS cc_start: 0.7359 (t) cc_final: 0.7127 (t) outliers start: 18 outliers final: 14 residues processed: 121 average time/residue: 0.0714 time to fit residues: 11.4663 Evaluate side-chains 123 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 69 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.111606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.098933 restraints weight = 15396.224| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.72 r_work: 0.3399 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6739 Z= 0.152 Angle : 0.718 19.672 9175 Z= 0.336 Chirality : 0.049 0.531 976 Planarity : 0.003 0.028 1177 Dihedral : 4.379 18.113 864 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.00 % Allowed : 16.31 % Favored : 81.69 % 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: 0.87 (0.31), residues: 792 helix: 1.24 (0.26), residues: 389 sheet: -0.60 (0.66), residues: 60 loop : 0.17 (0.37), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.018 0.001 TYR D 385 PHE 0.011 0.001 PHE D 369 TRP 0.015 0.001 TRP D 477 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6725) covalent geometry : angle 0.64224 / 0.32 ( 9140) SS BOND : bond 0.00297 / 0.14 ( 7) SS BOND : angle 1.23412 / 0.64 ( 14) hydrogen bonds : bond 0.04327 / 2.80 ( 323) hydrogen bonds : angle 4.93090 / 3.37 ( 906) link_NAG-ASN : bond 0.00964 / 0.63 ( 7) link_NAG-ASN : angle 6.66298 / 4.72 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1514.20 seconds wall clock time: 26 minutes 44.93 seconds (1604.93 seconds total)