Starting phenix.real_space_refine on Tue Aug 4 16:48:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12rp_76713/08_2026/12rp_76713.cif Found real_map, /net/cci-nas-00/data/ceres_data/12rp_76713/08_2026/12rp_76713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12rp_76713/08_2026/12rp_76713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12rp_76713/08_2026/12rp_76713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12rp_76713/08_2026/12rp_76713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12rp_76713/08_2026/12rp_76713.map" } resolution = 2.78 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= 0.000 sd= 0.014 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 18 5.16 5 C 3192 2.51 5 N 797 2.21 5 O 896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4903 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1590 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 14, 'TRANS': 180} Chain breaks: 2 Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1548 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 12, 'TRANS': 176} Chain: "B" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1709 Classifications: {'peptide': 211} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 10, 'TRANS': 200} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.95, per 1000 atoms: 0.19 Number of scatterers: 4903 At special positions: 0 Unit cell: (120.64, 87.36, 84.032, 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 18 16.00 O 896 8.00 N 797 7.00 C 3192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 529 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 234 " " NAG C1301 " - " ASN C 331 " Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 155.3 milliseconds 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 12.4% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.784A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.588A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.769A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.507A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.577A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 445 through 449 removed outlier: 3.690A pdb=" N ASN C 448 " --> pdb=" O ALA C 445 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR C 449 " --> pdb=" O ASP C 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 445 through 449' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.674A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.620A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.090A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.960A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.719A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N GLN B 134 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N LYS B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) 148 hydrogen bonds defined for protein. 357 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: 0.49 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1503 1.34 - 1.46: 1395 1.46 - 1.58: 2134 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 5050 Sorted by residual: bond pdb=" N HIS A 519 " pdb=" CA HIS A 519 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.71e+00 bond pdb=" N LYS A 528 " pdb=" CA LYS A 528 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.91e+00 bond pdb=" N LEU A 518 " pdb=" CA LEU A 518 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.41e-02 5.03e+03 5.98e+00 bond pdb=" N LEU A 517 " pdb=" CA LEU A 517 " ideal model delta sigma weight residual 1.464 1.487 -0.023 1.20e-02 6.94e+03 3.63e+00 bond pdb=" N ASN A 529 " pdb=" CA ASN A 529 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.28e+00 ... (remaining 5045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 6736 1.78 - 3.56: 118 3.56 - 5.34: 13 5.34 - 7.11: 1 7.11 - 8.89: 3 Bond angle restraints: 6871 Sorted by residual: angle pdb=" CB LYS B 113 " pdb=" CG LYS B 113 " pdb=" CD LYS B 113 " ideal model delta sigma weight residual 111.30 120.19 -8.89 2.30e+00 1.89e-01 1.49e+01 angle pdb=" CA LEU A 518 " pdb=" C LEU A 518 " pdb=" O LEU A 518 " ideal model delta sigma weight residual 121.40 117.36 4.04 1.11e+00 8.12e-01 1.32e+01 angle pdb=" CA GLN B 173 " pdb=" CB GLN B 173 " pdb=" CG GLN B 173 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.28e+01 angle pdb=" CA LYS A 528 " pdb=" C LYS A 528 " pdb=" O LYS A 528 " ideal model delta sigma weight residual 121.45 117.86 3.59 1.07e+00 8.73e-01 1.13e+01 angle pdb=" CA ASN B 121 " pdb=" CB ASN B 121 " pdb=" CG ASN B 121 " ideal model delta sigma weight residual 112.60 115.45 -2.85 1.00e+00 1.00e+00 8.12e+00 ... (remaining 6866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 2629 15.62 - 31.23: 271 31.23 - 46.85: 77 46.85 - 62.47: 17 62.47 - 78.09: 3 Dihedral angle restraints: 2997 sinusoidal: 1240 harmonic: 1757 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 125.37 -32.37 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -115.06 29.06 1 1.00e+01 1.00e-02 1.21e+01 dihedral pdb=" CA CYS C 336 " pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " ideal model delta sinusoidal sigma weight residual -73.00 -18.79 -54.21 1 2.00e+01 2.50e-03 9.96e+00 ... (remaining 2994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 561 0.048 - 0.096: 119 0.096 - 0.144: 54 0.144 - 0.192: 3 0.192 - 0.240: 1 Chirality restraints: 738 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 529 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ASN B 121 " pdb=" N ASN B 121 " pdb=" C ASN B 121 " pdb=" CB ASN B 121 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ASP B 198 " pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CB ASP B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 735 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 121 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.72e+00 pdb=" C ASN B 121 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN B 121 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 122 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 172 " 0.010 2.00e-02 2.50e+03 1.44e-02 3.64e+00 pdb=" CG PHE B 172 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 172 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 172 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B 172 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 172 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 172 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.020 2.00e-02 2.50e+03 1.68e-02 3.53e+00 pdb=" C7 NAG A1301 " -0.008 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.016 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.026 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.003 2.00e-02 2.50e+03 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 1878 2.88 - 3.38: 3853 3.38 - 3.89: 7569 3.89 - 4.39: 8712 4.39 - 4.90: 15386 Nonbonded interactions: 37398 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" O LEU A 518 " model vdw 2.371 3.040 nonbonded pdb=" O ASN B 121 " pdb=" OD1 ASN B 121 " model vdw 2.415 3.040 nonbonded pdb=" O THR A 470 " pdb=" OG1 THR A 470 " model vdw 2.560 3.040 nonbonded pdb=" O ASP B 198 " pdb=" OD1 ASP B 198 " model vdw 2.574 3.040 nonbonded pdb=" O THR C 470 " pdb=" OG1 THR C 470 " model vdw 2.582 3.040 ... (remaining 37393 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 329 through 517 or resid 1301)) selection = (chain 'C' and (resid 329 through 445 or resid 450 through 474 or resid 477 thro \ ugh 1301)) } 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: 6.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.180 Find NCS groups from input model: 0.070 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:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5062 Z= 0.181 Angle : 0.580 8.892 6899 Z= 0.319 Chirality : 0.047 0.240 738 Planarity : 0.004 0.036 879 Dihedral : 13.670 78.087 1847 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.94 % Allowed : 15.54 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.97 (0.34), residues: 577 helix: -2.72 (0.65), residues: 40 sheet: 1.07 (0.39), residues: 175 loop : -1.36 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 440 TYR 0.013 0.001 TYR B 170 PHE 0.033 0.001 PHE B 172 TRP 0.007 0.001 TRP B 64 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.18 ( 5050) covalent geometry : angle 0.57560 / 0.32 ( 6871) SS BOND : bond 0.00136 / 0.08 ( 8) SS BOND : angle 1.05766 / 0.59 ( 16) hydrogen bonds : bond 0.20608 / 12.75 ( 148) hydrogen bonds : angle 8.42268 / 6.10 ( 357) link_NAG-ASN : bond 0.00176 / 0.09 ( 4) link_NAG-ASN : angle 1.42380 / 0.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.8357 (mm) cc_final: 0.8107 (mt) REVERT: A 378 LYS cc_start: 0.8667 (mttt) cc_final: 0.8437 (ttmm) REVERT: A 444 LYS cc_start: 0.7893 (pttt) cc_final: 0.7289 (pmtt) REVERT: A 465 GLU cc_start: 0.8995 (tt0) cc_final: 0.8404 (tt0) REVERT: A 489 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: A 519 HIS cc_start: 0.7187 (m90) cc_final: 0.6966 (t70) REVERT: C 378 LYS cc_start: 0.8837 (mttt) cc_final: 0.8580 (mttm) REVERT: C 386 LYS cc_start: 0.8484 (mttm) cc_final: 0.6574 (pttt) REVERT: C 389 ASP cc_start: 0.8268 (m-30) cc_final: 0.7568 (m-30) REVERT: C 498 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.7809 (mmp80) REVERT: B 97 LYS cc_start: 0.9101 (ttpp) cc_final: 0.8742 (ttmt) REVERT: B 129 LYS cc_start: 0.8037 (mttt) cc_final: 0.7479 (mttt) REVERT: B 169 GLU cc_start: 0.8825 (tt0) cc_final: 0.7947 (tp30) REVERT: B 186 PHE cc_start: 0.7843 (p90) cc_final: 0.7622 (p90) REVERT: B 214 ARG cc_start: 0.8383 (mmt90) cc_final: 0.7900 (mmm160) outliers start: 5 outliers final: 2 residues processed: 84 average time/residue: 0.6898 time to fit residues: 59.7442 Evaluate side-chains 82 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain C residue 382 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.0000 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 overall best weight: 0.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS B 81 ASN B 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.067868 restraints weight = 9550.225| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.27 r_work: 0.2807 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5062 Z= 0.106 Angle : 0.495 7.854 6899 Z= 0.257 Chirality : 0.044 0.158 738 Planarity : 0.003 0.029 879 Dihedral : 4.654 52.995 745 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.87 % Allowed : 15.73 % Favored : 82.40 % 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: -0.96 (0.33), residues: 577 helix: -2.73 (0.59), residues: 47 sheet: 1.10 (0.37), residues: 176 loop : -1.32 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 440 TYR 0.006 0.001 TYR B 269 PHE 0.007 0.001 PHE B 65 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 5050) covalent geometry : angle 0.49054 / 0.26 ( 6871) SS BOND : bond 0.00125 / 0.08 ( 8) SS BOND : angle 0.74142 / 0.42 ( 16) hydrogen bonds : bond 0.03992 / 2.65 ( 148) hydrogen bonds : angle 6.47408 / 4.67 ( 357) link_NAG-ASN : bond 0.00102 / 0.05 ( 4) link_NAG-ASN : angle 1.46442 / 0.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.8281 (mm) cc_final: 0.8034 (mt) REVERT: A 444 LYS cc_start: 0.7921 (pttt) cc_final: 0.7299 (pmtt) REVERT: A 465 GLU cc_start: 0.8965 (tt0) cc_final: 0.8352 (tt0) REVERT: C 378 LYS cc_start: 0.8710 (mttt) cc_final: 0.8486 (tppt) REVERT: C 386 LYS cc_start: 0.8281 (mttm) cc_final: 0.6327 (pttt) REVERT: C 389 ASP cc_start: 0.8289 (m-30) cc_final: 0.7587 (m-30) REVERT: C 498 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.7776 (mmp80) REVERT: B 97 LYS cc_start: 0.9074 (ttpp) cc_final: 0.8762 (ttmt) REVERT: B 169 GLU cc_start: 0.8541 (tt0) cc_final: 0.8273 (tt0) REVERT: B 214 ARG cc_start: 0.8430 (mmt90) cc_final: 0.7886 (mmm160) outliers start: 10 outliers final: 4 residues processed: 92 average time/residue: 0.6263 time to fit residues: 59.6132 Evaluate side-chains 86 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain C residue 333 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 GLN B 66 HIS B 81 ASN B 165 ASN B 239 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065793 restraints weight = 9477.447| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.21 r_work: 0.2762 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 5062 Z= 0.198 Angle : 0.554 8.715 6899 Z= 0.287 Chirality : 0.047 0.174 738 Planarity : 0.004 0.028 879 Dihedral : 4.714 52.584 741 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.37 % Allowed : 15.92 % Favored : 80.71 % 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 (0.33), residues: 577 helix: -2.91 (0.56), residues: 47 sheet: 1.17 (0.38), residues: 167 loop : -1.37 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 440 TYR 0.011 0.001 TYR B 269 PHE 0.025 0.001 PHE B 186 TRP 0.010 0.001 TRP B 64 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 ( 5050) covalent geometry : angle 0.54842 / 0.29 ( 6871) SS BOND : bond 0.00199 / 0.10 ( 8) SS BOND : angle 1.21816 / 0.69 ( 16) hydrogen bonds : bond 0.04255 / 2.82 ( 148) hydrogen bonds : angle 6.21075 / 4.45 ( 357) link_NAG-ASN : bond 0.00172 / 0.08 ( 4) link_NAG-ASN : angle 1.54473 / 0.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.8306 (mm) cc_final: 0.8086 (mt) REVERT: A 444 LYS cc_start: 0.7931 (pttt) cc_final: 0.7301 (pmtt) REVERT: A 465 GLU cc_start: 0.9012 (tt0) cc_final: 0.8403 (tt0) REVERT: C 378 LYS cc_start: 0.8719 (mttt) cc_final: 0.8486 (ttmm) REVERT: C 386 LYS cc_start: 0.8429 (mttm) cc_final: 0.6564 (pttt) REVERT: C 389 ASP cc_start: 0.8442 (m-30) cc_final: 0.7724 (m-30) REVERT: C 498 ARG cc_start: 0.8393 (mmm-85) cc_final: 0.7705 (mmp80) REVERT: B 169 GLU cc_start: 0.8595 (tt0) cc_final: 0.8294 (tt0) REVERT: B 214 ARG cc_start: 0.8392 (mmt90) cc_final: 0.7877 (mmm160) outliers start: 18 outliers final: 10 residues processed: 95 average time/residue: 0.6015 time to fit residues: 59.2622 Evaluate side-chains 90 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 172 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 22 optimal weight: 0.0010 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS B 81 ASN B 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.094022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.066976 restraints weight = 9517.475| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.20 r_work: 0.2791 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5062 Z= 0.127 Angle : 0.521 8.854 6899 Z= 0.267 Chirality : 0.045 0.165 738 Planarity : 0.003 0.026 879 Dihedral : 4.596 53.323 741 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.06 % Allowed : 17.98 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.97 (0.33), residues: 577 helix: -2.85 (0.58), residues: 47 sheet: 1.21 (0.38), residues: 167 loop : -1.32 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 440 TYR 0.008 0.001 TYR B 269 PHE 0.022 0.001 PHE B 172 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 5050) covalent geometry : angle 0.51586 / 0.27 ( 6871) SS BOND : bond 0.00121 / 0.07 ( 8) SS BOND : angle 0.99027 / 0.55 ( 16) hydrogen bonds : bond 0.03486 / 2.35 ( 148) hydrogen bonds : angle 6.01911 / 4.31 ( 357) link_NAG-ASN : bond 0.00113 / 0.06 ( 4) link_NAG-ASN : angle 1.49155 / 0.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.8336 (mm) cc_final: 0.8115 (mt) REVERT: A 444 LYS cc_start: 0.7959 (pttt) cc_final: 0.7443 (pmtt) REVERT: A 465 GLU cc_start: 0.9005 (tt0) cc_final: 0.8406 (tt0) REVERT: A 489 TYR cc_start: 0.8170 (m-80) cc_final: 0.7963 (m-80) REVERT: C 378 LYS cc_start: 0.8738 (mttt) cc_final: 0.8506 (ttmm) REVERT: C 386 LYS cc_start: 0.8399 (mttm) cc_final: 0.6559 (pttt) REVERT: C 389 ASP cc_start: 0.8326 (m-30) cc_final: 0.7592 (m-30) REVERT: C 498 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.7886 (mmp80) REVERT: B 97 LYS cc_start: 0.9106 (ttpp) cc_final: 0.8677 (ttmm) REVERT: B 169 GLU cc_start: 0.8531 (tt0) cc_final: 0.8256 (tt0) REVERT: B 186 PHE cc_start: 0.7682 (p90) cc_final: 0.7426 (p90) REVERT: B 214 ARG cc_start: 0.8385 (mmt90) cc_final: 0.7842 (mmm160) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.6017 time to fit residues: 56.0269 Evaluate side-chains 88 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 172 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.065935 restraints weight = 9634.760| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.26 r_work: 0.2788 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5062 Z= 0.165 Angle : 0.541 8.969 6899 Z= 0.278 Chirality : 0.046 0.166 738 Planarity : 0.004 0.026 879 Dihedral : 4.673 53.102 741 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.00 % Allowed : 17.42 % Favored : 79.59 % 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: -0.96 (0.33), residues: 577 helix: -2.87 (0.57), residues: 47 sheet: 1.24 (0.39), residues: 167 loop : -1.33 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 440 TYR 0.009 0.001 TYR B 269 PHE 0.022 0.001 PHE B 172 TRP 0.008 0.001 TRP B 64 HIS 0.002 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 5050) covalent geometry : angle 0.53583 / 0.28 ( 6871) SS BOND : bond 0.00129 / 0.07 ( 8) SS BOND : angle 1.06777 / 0.60 ( 16) hydrogen bonds : bond 0.03758 / 2.53 ( 148) hydrogen bonds : angle 5.96717 / 4.26 ( 357) link_NAG-ASN : bond 0.00139 / 0.07 ( 4) link_NAG-ASN : angle 1.52038 / 0.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.8339 (mm) cc_final: 0.8124 (mt) REVERT: A 444 LYS cc_start: 0.7955 (pttt) cc_final: 0.7423 (pmtt) REVERT: A 465 GLU cc_start: 0.9001 (tt0) cc_final: 0.8362 (tt0) REVERT: C 378 LYS cc_start: 0.8752 (mttt) cc_final: 0.8493 (ttmm) REVERT: C 386 LYS cc_start: 0.8410 (mttm) cc_final: 0.6575 (pttt) REVERT: C 389 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7650 (m-30) REVERT: C 498 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.7844 (mmp80) REVERT: B 97 LYS cc_start: 0.9102 (ttpp) cc_final: 0.8680 (ttmm) REVERT: B 169 GLU cc_start: 0.8545 (tt0) cc_final: 0.8257 (tt0) REVERT: B 186 PHE cc_start: 0.7709 (p90) cc_final: 0.7419 (p90) REVERT: B 214 ARG cc_start: 0.8404 (mmt90) cc_final: 0.7853 (mmm160) outliers start: 16 outliers final: 13 residues processed: 90 average time/residue: 0.5837 time to fit residues: 54.3175 Evaluate side-chains 95 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 172 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS B 81 ASN B 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.091792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.064509 restraints weight = 9752.239| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.27 r_work: 0.2759 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 5062 Z= 0.238 Angle : 0.596 9.464 6899 Z= 0.308 Chirality : 0.048 0.172 738 Planarity : 0.004 0.027 879 Dihedral : 4.926 52.891 741 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.49 % Allowed : 15.92 % Favored : 79.59 % 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: -1.06 (0.33), residues: 577 helix: -2.99 (0.55), residues: 47 sheet: 1.16 (0.39), residues: 167 loop : -1.37 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 440 TYR 0.012 0.001 TYR B 269 PHE 0.021 0.001 PHE B 172 TRP 0.011 0.001 TRP B 64 HIS 0.002 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 ( 5050) covalent geometry : angle 0.59093 / 0.31 ( 6871) SS BOND : bond 0.00143 / 0.08 ( 8) SS BOND : angle 1.18906 / 0.67 ( 16) hydrogen bonds : bond 0.04182 / 2.77 ( 148) hydrogen bonds : angle 6.07564 / 4.34 ( 357) link_NAG-ASN : bond 0.00222 / 0.11 ( 4) link_NAG-ASN : angle 1.64353 / 1.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.8368 (mm) cc_final: 0.8153 (mt) REVERT: A 444 LYS cc_start: 0.7920 (pttt) cc_final: 0.7388 (pmtt) REVERT: A 465 GLU cc_start: 0.9060 (tt0) cc_final: 0.8453 (tt0) REVERT: A 489 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: C 378 LYS cc_start: 0.8755 (mttt) cc_final: 0.8532 (ttmm) REVERT: C 386 LYS cc_start: 0.8484 (mttm) cc_final: 0.6570 (pttt) REVERT: C 389 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: C 498 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.7768 (mmp80) REVERT: B 169 GLU cc_start: 0.8595 (tt0) cc_final: 0.8301 (tt0) REVERT: B 187 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8036 (t) REVERT: B 214 ARG cc_start: 0.8433 (mmt90) cc_final: 0.7842 (mmm160) outliers start: 24 outliers final: 16 residues processed: 98 average time/residue: 0.5098 time to fit residues: 51.8605 Evaluate side-chains 99 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS B 81 ASN B 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.093726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.066799 restraints weight = 9621.672| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.20 r_work: 0.2789 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5062 Z= 0.128 Angle : 0.550 9.275 6899 Z= 0.282 Chirality : 0.045 0.172 738 Planarity : 0.003 0.026 879 Dihedral : 4.719 53.824 741 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.37 % Allowed : 17.60 % Favored : 79.03 % 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 (0.33), residues: 577 helix: -2.88 (0.58), residues: 47 sheet: 1.30 (0.39), residues: 163 loop : -1.30 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 440 TYR 0.007 0.001 TYR B 279 PHE 0.027 0.001 PHE B 186 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 5050) covalent geometry : angle 0.54547 / 0.28 ( 6871) SS BOND : bond 0.00088 / 0.05 ( 8) SS BOND : angle 0.94492 / 0.53 ( 16) hydrogen bonds : bond 0.03338 / 2.27 ( 148) hydrogen bonds : angle 5.92224 / 4.24 ( 357) link_NAG-ASN : bond 0.00117 / 0.06 ( 4) link_NAG-ASN : angle 1.56251 / 0.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.8358 (mm) cc_final: 0.8145 (mt) REVERT: A 444 LYS cc_start: 0.7945 (pttt) cc_final: 0.7453 (pmtt) REVERT: A 465 GLU cc_start: 0.9013 (tt0) cc_final: 0.8412 (tt0) REVERT: A 489 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: C 378 LYS cc_start: 0.8742 (mttt) cc_final: 0.8539 (ttmm) REVERT: C 386 LYS cc_start: 0.8373 (mttm) cc_final: 0.6523 (pttt) REVERT: C 389 ASP cc_start: 0.8397 (m-30) cc_final: 0.7576 (m-30) REVERT: C 498 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.7843 (mmp80) REVERT: B 97 LYS cc_start: 0.9113 (ttpp) cc_final: 0.8683 (ttmm) REVERT: B 169 GLU cc_start: 0.8546 (tt0) cc_final: 0.8278 (tt0) REVERT: B 186 PHE cc_start: 0.7729 (p90) cc_final: 0.7387 (p90) REVERT: B 187 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.7999 (t) REVERT: B 214 ARG cc_start: 0.8408 (mmt90) cc_final: 0.7862 (mmm160) outliers start: 18 outliers final: 15 residues processed: 91 average time/residue: 0.6760 time to fit residues: 63.5855 Evaluate side-chains 99 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 16 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.093749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.066580 restraints weight = 9668.890| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.28 r_work: 0.2804 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5062 Z= 0.136 Angle : 0.551 9.028 6899 Z= 0.282 Chirality : 0.046 0.171 738 Planarity : 0.004 0.026 879 Dihedral : 4.644 53.277 741 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.93 % Allowed : 17.04 % Favored : 79.03 % 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: -0.95 (0.33), residues: 577 helix: -2.88 (0.58), residues: 47 sheet: 1.19 (0.39), residues: 167 loop : -1.28 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 440 TYR 0.008 0.001 TYR C 501 PHE 0.024 0.001 PHE B 186 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 5050) covalent geometry : angle 0.54618 / 0.28 ( 6871) SS BOND : bond 0.00123 / 0.08 ( 8) SS BOND : angle 0.97989 / 0.55 ( 16) hydrogen bonds : bond 0.03394 / 2.30 ( 148) hydrogen bonds : angle 5.81625 / 4.17 ( 357) link_NAG-ASN : bond 0.00110 / 0.05 ( 4) link_NAG-ASN : angle 1.51026 / 0.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.8360 (mm) cc_final: 0.8151 (mt) REVERT: A 444 LYS cc_start: 0.7948 (pttt) cc_final: 0.7458 (pmtt) REVERT: A 465 GLU cc_start: 0.9004 (tt0) cc_final: 0.8402 (tt0) REVERT: A 489 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: C 378 LYS cc_start: 0.8741 (mttt) cc_final: 0.8533 (ttmm) REVERT: C 386 LYS cc_start: 0.8352 (mttm) cc_final: 0.6535 (pttt) REVERT: C 389 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: C 498 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.7831 (mmp80) REVERT: B 97 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8670 (ttmm) REVERT: B 169 GLU cc_start: 0.8549 (tt0) cc_final: 0.8244 (tt0) REVERT: B 214 ARG cc_start: 0.8409 (mmt90) cc_final: 0.7851 (mmm160) outliers start: 21 outliers final: 17 residues processed: 92 average time/residue: 0.6508 time to fit residues: 62.0879 Evaluate side-chains 99 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.0060 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.094734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.067550 restraints weight = 9545.310| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.27 r_work: 0.2801 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5062 Z= 0.114 Angle : 0.544 8.863 6899 Z= 0.278 Chirality : 0.045 0.170 738 Planarity : 0.003 0.026 879 Dihedral : 4.545 53.754 741 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.00 % Allowed : 17.98 % Favored : 79.03 % 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: -0.89 (0.33), residues: 577 helix: -2.83 (0.60), residues: 47 sheet: 1.21 (0.39), residues: 167 loop : -1.23 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 440 TYR 0.006 0.001 TYR A 489 PHE 0.023 0.001 PHE B 172 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 5050) covalent geometry : angle 0.54070 / 0.28 ( 6871) SS BOND : bond 0.00116 / 0.08 ( 8) SS BOND : angle 0.80454 / 0.45 ( 16) hydrogen bonds : bond 0.03113 / 2.13 ( 148) hydrogen bonds : angle 5.72587 / 4.11 ( 357) link_NAG-ASN : bond 0.00102 / 0.05 ( 4) link_NAG-ASN : angle 1.45005 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.8348 (mm) cc_final: 0.8135 (mt) REVERT: A 444 LYS cc_start: 0.7941 (pttt) cc_final: 0.7443 (pmtt) REVERT: A 465 GLU cc_start: 0.9003 (tt0) cc_final: 0.8403 (tt0) REVERT: C 378 LYS cc_start: 0.8735 (mttt) cc_final: 0.8503 (ttmm) REVERT: C 386 LYS cc_start: 0.8314 (mttm) cc_final: 0.6501 (pttt) REVERT: C 389 ASP cc_start: 0.8400 (m-30) cc_final: 0.7567 (m-30) REVERT: C 498 ARG cc_start: 0.8519 (mmm-85) cc_final: 0.7938 (mmp80) REVERT: B 97 LYS cc_start: 0.9094 (ttpp) cc_final: 0.8660 (ttmm) REVERT: B 169 GLU cc_start: 0.8510 (tt0) cc_final: 0.8248 (tt0) REVERT: B 186 PHE cc_start: 0.7690 (p90) cc_final: 0.7418 (p90) REVERT: B 187 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.7966 (t) REVERT: B 214 ARG cc_start: 0.8383 (mmt90) cc_final: 0.7844 (mmm160) outliers start: 16 outliers final: 12 residues processed: 90 average time/residue: 0.6943 time to fit residues: 64.5957 Evaluate side-chains 95 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 36 optimal weight: 0.0040 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.0030 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.095078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.068053 restraints weight = 9641.789| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.23 r_work: 0.2814 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5062 Z= 0.109 Angle : 0.527 8.570 6899 Z= 0.273 Chirality : 0.045 0.166 738 Planarity : 0.004 0.036 879 Dihedral : 4.444 53.330 741 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.06 % Allowed : 18.73 % Favored : 79.21 % 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: -0.88 (0.33), residues: 577 helix: -2.87 (0.58), residues: 47 sheet: 1.22 (0.39), residues: 167 loop : -1.22 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 440 TYR 0.006 0.001 TYR B 269 PHE 0.023 0.001 PHE B 172 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 5050) covalent geometry : angle 0.52368 / 0.27 ( 6871) SS BOND : bond 0.00127 / 0.09 ( 8) SS BOND : angle 0.77293 / 0.43 ( 16) hydrogen bonds : bond 0.03060 / 2.11 ( 148) hydrogen bonds : angle 5.75774 / 4.10 ( 357) link_NAG-ASN : bond 0.00098 / 0.05 ( 4) link_NAG-ASN : angle 1.38964 / 0.86 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1154 Ramachandran restraints generated. 577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.8368 (mm) cc_final: 0.8153 (mt) REVERT: A 444 LYS cc_start: 0.7941 (pttt) cc_final: 0.7459 (pmtt) REVERT: A 465 GLU cc_start: 0.8990 (tt0) cc_final: 0.8407 (tt0) REVERT: C 378 LYS cc_start: 0.8739 (mttt) cc_final: 0.8511 (ttmm) REVERT: C 386 LYS cc_start: 0.8361 (mttm) cc_final: 0.6555 (pttt) REVERT: C 389 ASP cc_start: 0.8312 (m-30) cc_final: 0.7531 (m-30) REVERT: C 498 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.7974 (mmp80) REVERT: B 97 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8681 (ttmm) REVERT: B 169 GLU cc_start: 0.8537 (tt0) cc_final: 0.8238 (tt0) REVERT: B 186 PHE cc_start: 0.7680 (p90) cc_final: 0.7415 (p90) REVERT: B 187 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.7960 (t) REVERT: B 214 ARG cc_start: 0.8400 (mmt90) cc_final: 0.7860 (mmm160) outliers start: 11 outliers final: 10 residues processed: 90 average time/residue: 0.6986 time to fit residues: 65.0798 Evaluate side-chains 92 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain B residue 164 LYS Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.093326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.066008 restraints weight = 9627.329| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.26 r_work: 0.2770 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5062 Z= 0.194 Angle : 0.589 8.974 6899 Z= 0.306 Chirality : 0.047 0.171 738 Planarity : 0.004 0.036 879 Dihedral : 4.633 53.078 741 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.62 % Allowed : 18.73 % Favored : 78.65 % 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: -0.97 (0.33), residues: 577 helix: -3.04 (0.54), residues: 47 sheet: 1.10 (0.39), residues: 171 loop : -1.24 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 440 TYR 0.010 0.001 TYR B 279 PHE 0.037 0.001 PHE B 168 TRP 0.009 0.001 TRP B 64 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 ( 5050) covalent geometry : angle 0.58474 / 0.30 ( 6871) SS BOND : bond 0.00124 / 0.07 ( 8) SS BOND : angle 1.09114 / 0.61 ( 16) hydrogen bonds : bond 0.03665 / 2.47 ( 148) hydrogen bonds : angle 5.92649 / 4.17 ( 357) link_NAG-ASN : bond 0.00142 / 0.07 ( 4) link_NAG-ASN : angle 1.46410 / 0.91 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1957.29 seconds wall clock time: 34 minutes 7.78 seconds (2047.78 seconds total)