Starting phenix.real_space_refine on Thu Jul 2 00:08:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hnc_34910/07_2026/8hnc_34910.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnc_34910/07_2026/8hnc_34910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8hnc_34910/07_2026/8hnc_34910.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hnc_34910/07_2026/8hnc_34910.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hnc_34910/07_2026/8hnc_34910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnc_34910/07_2026/8hnc_34910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hnc_34910/07_2026/8hnc_34910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnc_34910/07_2026/8hnc_34910.map" } resolution = 3.73 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= 0.041 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 33 5.16 5 C 2825 2.51 5 N 678 2.21 5 O 736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s 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: 4272 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4187 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 21, 'TRANS': 548} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 4, 'TYR:plan': 5, 'ASP:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 10} Unresolved non-hydrogen planarities: 132 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 chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'BLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.92, per 1000 atoms: 0.22 Number of scatterers: 4272 At special positions: 0 Unit cell: (101.504, 59.904, 79.872, 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 33 16.00 O 736 8.00 N 678 7.00 C 2825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.04 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.01 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 704 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 180.3 milliseconds 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 1 sheets defined 66.1% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 26 through 49 removed outlier: 4.087A pdb=" N PHE A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 58 Processing helix chain 'A' and resid 62 through 79 removed outlier: 4.505A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.946A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 92 through 113 Processing helix chain 'A' and resid 114 through 117 Processing helix chain 'A' and resid 121 through 125 removed outlier: 4.652A pdb=" N LYS A 125 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.085A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 removed outlier: 3.844A pdb=" N SER A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 258 through 274 removed outlier: 3.594A pdb=" N PHE A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.815A pdb=" N LEU A 279 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 335 through 366 removed outlier: 5.253A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 400 removed outlier: 3.757A pdb=" N GLY A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 403 through 426 removed outlier: 3.767A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 550 removed outlier: 3.827A pdb=" N LYS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 removed outlier: 3.537A pdb=" N VAL A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 567 through 584 Processing helix chain 'A' and resid 586 through 597 Processing helix chain 'A' and resid 617 through 651 Processing sheet with id=AA1, first strand: chain 'A' and resid 480 through 481 263 hydrogen bonds defined for protein. 777 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: 0.67 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 664 1.32 - 1.45: 1233 1.45 - 1.57: 2432 1.57 - 1.69: 0 1.69 - 1.82: 49 Bond restraints: 4378 Sorted by residual: bond pdb=" CGD BLR A 701 " pdb=" O1D BLR A 701 " ideal model delta sigma weight residual 1.231 1.308 -0.077 2.00e-02 2.50e+03 1.46e+01 bond pdb=" N LEU A 545 " pdb=" CA LEU A 545 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.28e-02 6.10e+03 1.31e+01 bond pdb=" C TYR A 352 " pdb=" O TYR A 352 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" CA LEU A 545 " pdb=" C LEU A 545 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.35e-02 5.49e+03 9.96e+00 bond pdb=" CA TYR A 352 " pdb=" C TYR A 352 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.32e-02 5.74e+03 9.53e+00 ... (remaining 4373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 5701 2.22 - 4.44: 206 4.44 - 6.66: 32 6.66 - 8.88: 9 8.88 - 11.10: 3 Bond angle restraints: 5951 Sorted by residual: angle pdb=" N VAL A 509 " pdb=" CA VAL A 509 " pdb=" C VAL A 509 " ideal model delta sigma weight residual 110.62 118.68 -8.06 1.02e+00 9.61e-01 6.25e+01 angle pdb=" N ASN A 503 " pdb=" CA ASN A 503 " pdb=" C ASN A 503 " ideal model delta sigma weight residual 111.56 122.66 -11.10 1.43e+00 4.89e-01 6.02e+01 angle pdb=" C THR A 186 " pdb=" N PRO A 187 " pdb=" CA PRO A 187 " ideal model delta sigma weight residual 121.65 115.05 6.60 1.01e+00 9.80e-01 4.27e+01 angle pdb=" C TRP A 254 " pdb=" N VAL A 255 " pdb=" CA VAL A 255 " ideal model delta sigma weight residual 122.99 114.19 8.80 1.39e+00 5.18e-01 4.01e+01 angle pdb=" C THR A 510 " pdb=" N GLY A 511 " pdb=" CA GLY A 511 " ideal model delta sigma weight residual 121.58 116.85 4.73 8.60e-01 1.35e+00 3.02e+01 ... (remaining 5946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 2283 18.00 - 36.00: 175 36.00 - 54.00: 34 54.00 - 72.00: 3 72.00 - 89.99: 5 Dihedral angle restraints: 2500 sinusoidal: 873 harmonic: 1627 Sorted by residual: dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 506 " pdb=" CB CYS A 506 " ideal model delta sinusoidal sigma weight residual 93.00 175.59 -82.59 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 463 " pdb=" CB CYS A 463 " ideal model delta sinusoidal sigma weight residual 93.00 14.62 78.38 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" C LEU A 143 " pdb=" N LEU A 143 " pdb=" CA LEU A 143 " pdb=" CB LEU A 143 " ideal model delta harmonic sigma weight residual -122.60 -110.31 -12.29 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 2497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 691 0.294 - 0.587: 3 0.587 - 0.881: 0 0.881 - 1.175: 0 1.175 - 1.468: 1 Chirality restraints: 695 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-02 2.50e+03 5.39e+03 chirality pdb=" CA ASN A 503 " pdb=" N ASN A 503 " pdb=" C ASN A 503 " pdb=" CB ASN A 503 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ASN A 460 " pdb=" N ASN A 460 " pdb=" C ASN A 460 " pdb=" CB ASN A 460 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 692 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.313 2.00e-02 2.50e+03 2.66e-01 8.82e+02 pdb=" C7 NAG B 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.463 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.286 2.00e-02 2.50e+03 2.44e-01 7.46e+02 pdb=" C7 NAG B 1 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.018 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.412 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " -0.159 2.00e-02 2.50e+03 1.31e-01 2.14e+02 pdb=" C7 NAG A 704 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " -0.118 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " 0.210 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " 0.022 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 53 2.64 - 3.21: 4287 3.21 - 3.77: 6608 3.77 - 4.34: 8538 4.34 - 4.90: 13867 Nonbonded interactions: 33353 Sorted by model distance: nonbonded pdb=" ND BLR A 701 " pdb=" O2A BLR A 701 " model vdw 2.079 3.120 nonbonded pdb=" O MET A 233 " pdb=" N ALA A 257 " model vdw 2.204 3.120 nonbonded pdb=" O ASN A 460 " pdb=" N CYS A 463 " model vdw 2.224 3.120 nonbonded pdb=" OG SER A 418 " pdb=" ND2 ASN A 544 " model vdw 2.293 3.120 nonbonded pdb=" ND1 HIS A 115 " pdb=" CD1 TRP A 259 " model vdw 2.364 3.340 ... (remaining 33348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.500 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.382 4388 Z= 0.463 Angle : 1.277 52.004 5974 Z= 0.691 Chirality : 0.081 1.468 695 Planarity : 0.015 0.266 726 Dihedral : 12.995 89.994 1443 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.49 % Allowed : 5.11 % Favored : 94.40 % Cbeta Deviations : 0.39 % 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: -2.79 (0.31), residues: 562 helix: -1.27 (0.24), residues: 343 sheet: None (None), residues: 0 loop : -2.72 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 57 TYR 0.025 0.002 TYR A 352 PHE 0.029 0.001 PHE A 591 TRP 0.006 0.001 TRP A 258 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.36 ( 4378) covalent geometry : angle 1.00940 / 0.64 ( 5951) SS BOND : bond 0.00877 / 0.39 ( 7) SS BOND : angle 1.36399 / 0.88 ( 14) hydrogen bonds : bond 0.15315 / 10.01 ( 263) hydrogen bonds : angle 7.41183 / 5.21 ( 777) link_BETA1-4 : bond 0.38155 / 20.08 ( 1) link_BETA1-4 : angle 31.45835 / 18.09 ( 3) link_NAG-ASN : bond 0.00145 / 0.07 ( 2) link_NAG-ASN : angle 10.72764 / 7.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8898 (tpt) cc_final: 0.8483 (tpp) REVERT: A 185 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 381 ILE cc_start: 0.8682 (tp) cc_final: 0.8425 (tp) REVERT: A 617 ASN cc_start: 0.7996 (t0) cc_final: 0.7607 (t0) outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.0808 time to fit residues: 10.5723 Evaluate side-chains 76 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.207474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.156794 restraints weight = 4888.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.160858 restraints weight = 2972.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.163589 restraints weight = 2198.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.165285 restraints weight = 1826.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.166015 restraints weight = 1639.619| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4388 Z= 0.153 Angle : 0.689 13.800 5974 Z= 0.324 Chirality : 0.044 0.267 695 Planarity : 0.004 0.039 726 Dihedral : 7.083 86.793 617 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.46 % Allowed : 14.11 % Favored : 84.43 % 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: -0.51 (0.34), residues: 562 helix: 0.55 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -1.80 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 526 TYR 0.028 0.002 TYR A 590 PHE 0.013 0.001 PHE A 591 TRP 0.006 0.001 TRP A 259 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 4378) covalent geometry : angle 0.64943 / 0.32 ( 5951) SS BOND : bond 0.00192 / 0.10 ( 7) SS BOND : angle 1.06806 / 0.86 ( 14) hydrogen bonds : bond 0.04764 / 3.11 ( 263) hydrogen bonds : angle 4.85056 / 3.42 ( 777) link_BETA1-4 : bond 0.00534 / 0.28 ( 1) link_BETA1-4 : angle 9.18158 / 5.74 ( 3) link_NAG-ASN : bond 0.00300 / 0.15 ( 2) link_NAG-ASN : angle 3.02046 / 1.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8963 (tpt) cc_final: 0.8535 (tpp) REVERT: A 254 TRP cc_start: 0.7894 (t-100) cc_final: 0.7665 (t-100) REVERT: A 381 ILE cc_start: 0.8745 (tp) cc_final: 0.8436 (tp) REVERT: A 390 MET cc_start: 0.8371 (mmt) cc_final: 0.7813 (mmt) outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 0.0507 time to fit residues: 5.7584 Evaluate side-chains 80 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 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 = 0.3980 r_free = 0.3980 target = 0.185461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128630 restraints weight = 4998.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.132333 restraints weight = 3283.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134455 restraints weight = 2543.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.136225 restraints weight = 2187.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137011 restraints weight = 1994.981| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4388 Z= 0.138 Angle : 0.634 11.192 5974 Z= 0.297 Chirality : 0.043 0.282 695 Planarity : 0.004 0.040 726 Dihedral : 6.664 81.698 617 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.92 % Allowed : 16.55 % Favored : 80.54 % 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: 0.39 (0.36), residues: 562 helix: 1.32 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.45 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 526 TYR 0.024 0.002 TYR A 590 PHE 0.013 0.001 PHE A 591 TRP 0.006 0.001 TRP A 254 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4378) covalent geometry : angle 0.60459 / 0.29 ( 5951) SS BOND : bond 0.00113 / 0.06 ( 7) SS BOND : angle 0.67465 / 0.52 ( 14) hydrogen bonds : bond 0.04274 / 2.81 ( 263) hydrogen bonds : angle 4.40166 / 3.10 ( 777) link_BETA1-4 : bond 0.00704 / 0.37 ( 1) link_BETA1-4 : angle 7.21260 / 4.32 ( 3) link_NAG-ASN : bond 0.00192 / 0.09 ( 2) link_NAG-ASN : angle 3.19626 / 1.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8792 (tpt) cc_final: 0.8394 (tpp) REVERT: A 170 MET cc_start: 0.7961 (mmm) cc_final: 0.7656 (mmm) REVERT: A 254 TRP cc_start: 0.8049 (t-100) cc_final: 0.7771 (t-100) REVERT: A 381 ILE cc_start: 0.8560 (tp) cc_final: 0.8261 (tp) REVERT: A 390 MET cc_start: 0.8180 (mmt) cc_final: 0.7531 (mmt) outliers start: 12 outliers final: 7 residues processed: 87 average time/residue: 0.0505 time to fit residues: 5.9749 Evaluate side-chains 84 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.216238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.167327 restraints weight = 4795.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.170906 restraints weight = 3030.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.173466 restraints weight = 2282.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.174771 restraints weight = 1922.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.175128 restraints weight = 1739.232| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4388 Z= 0.127 Angle : 0.607 9.830 5974 Z= 0.288 Chirality : 0.043 0.242 695 Planarity : 0.003 0.039 726 Dihedral : 6.465 78.761 617 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.68 % Allowed : 17.76 % Favored : 79.56 % 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: 0.65 (0.36), residues: 562 helix: 1.50 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -1.38 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 526 TYR 0.024 0.001 TYR A 590 PHE 0.011 0.001 PHE A 591 TRP 0.006 0.001 TRP A 254 HIS 0.002 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 4378) covalent geometry : angle 0.58152 / 0.28 ( 5951) SS BOND : bond 0.00114 / 0.05 ( 7) SS BOND : angle 0.79504 / 0.66 ( 14) hydrogen bonds : bond 0.04073 / 2.69 ( 263) hydrogen bonds : angle 4.22407 / 2.98 ( 777) link_BETA1-4 : bond 0.00744 / 0.39 ( 1) link_BETA1-4 : angle 6.21184 / 3.67 ( 3) link_NAG-ASN : bond 0.00221 / 0.11 ( 2) link_NAG-ASN : angle 3.23721 / 1.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8933 (tpt) cc_final: 0.8556 (tpp) REVERT: A 170 MET cc_start: 0.7777 (mmm) cc_final: 0.7479 (mmm) REVERT: A 254 TRP cc_start: 0.7976 (t-100) cc_final: 0.7768 (t-100) REVERT: A 381 ILE cc_start: 0.8769 (tp) cc_final: 0.8460 (tp) REVERT: A 390 MET cc_start: 0.8225 (mmt) cc_final: 0.7613 (mmt) outliers start: 11 outliers final: 6 residues processed: 88 average time/residue: 0.0539 time to fit residues: 6.3301 Evaluate side-chains 86 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 51 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.216329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.166213 restraints weight = 4810.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.170298 restraints weight = 2899.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.172570 restraints weight = 2123.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.174502 restraints weight = 1778.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.175096 restraints weight = 1588.322| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4388 Z= 0.131 Angle : 0.596 9.066 5974 Z= 0.285 Chirality : 0.042 0.238 695 Planarity : 0.003 0.039 726 Dihedral : 6.287 76.577 617 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.14 % Allowed : 18.25 % Favored : 77.62 % 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 (0.36), residues: 562 helix: 1.64 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.18 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 58 TYR 0.023 0.002 TYR A 590 PHE 0.011 0.001 PHE A 591 TRP 0.010 0.001 TRP A 254 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 4378) covalent geometry : angle 0.57208 / 0.28 ( 5951) SS BOND : bond 0.00181 / 0.08 ( 7) SS BOND : angle 1.16549 / 0.84 ( 14) hydrogen bonds : bond 0.03951 / 2.61 ( 263) hydrogen bonds : angle 4.13045 / 2.91 ( 777) link_BETA1-4 : bond 0.00511 / 0.27 ( 1) link_BETA1-4 : angle 5.60233 / 3.26 ( 3) link_NAG-ASN : bond 0.00322 / 0.16 ( 2) link_NAG-ASN : angle 3.19050 / 1.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8891 (tpt) cc_final: 0.8512 (tpp) REVERT: A 95 LYS cc_start: 0.8475 (mttt) cc_final: 0.8271 (ttmm) REVERT: A 254 TRP cc_start: 0.8028 (t-100) cc_final: 0.7540 (t60) REVERT: A 381 ILE cc_start: 0.8726 (tp) cc_final: 0.8421 (tp) REVERT: A 390 MET cc_start: 0.8187 (mmt) cc_final: 0.7455 (mmt) outliers start: 17 outliers final: 9 residues processed: 91 average time/residue: 0.0540 time to fit residues: 6.5137 Evaluate side-chains 89 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.180549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.123337 restraints weight = 5047.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.126466 restraints weight = 3485.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.128635 restraints weight = 2799.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.129593 restraints weight = 2448.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.130523 restraints weight = 2276.671| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4388 Z= 0.141 Angle : 0.636 10.159 5974 Z= 0.298 Chirality : 0.043 0.237 695 Planarity : 0.003 0.039 726 Dihedral : 6.172 76.588 617 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.89 % Allowed : 19.71 % Favored : 76.40 % 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: 1.05 (0.37), residues: 562 helix: 1.77 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.12 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 526 TYR 0.023 0.002 TYR A 590 PHE 0.010 0.001 PHE A 116 TRP 0.010 0.001 TRP A 254 HIS 0.002 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 4378) covalent geometry : angle 0.61569 / 0.29 ( 5951) SS BOND : bond 0.00262 / 0.13 ( 7) SS BOND : angle 1.59226 / 1.06 ( 14) hydrogen bonds : bond 0.04007 / 2.66 ( 263) hydrogen bonds : angle 4.14285 / 2.92 ( 777) link_BETA1-4 : bond 0.00416 / 0.22 ( 1) link_BETA1-4 : angle 5.19343 / 3.03 ( 3) link_NAG-ASN : bond 0.00280 / 0.14 ( 2) link_NAG-ASN : angle 2.73830 / 1.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8788 (tpt) cc_final: 0.8395 (tpp) REVERT: A 170 MET cc_start: 0.7627 (mmm) cc_final: 0.7288 (mmm) REVERT: A 254 TRP cc_start: 0.8125 (t-100) cc_final: 0.7607 (t60) REVERT: A 381 ILE cc_start: 0.8593 (tp) cc_final: 0.8276 (tp) REVERT: A 390 MET cc_start: 0.8132 (mmt) cc_final: 0.7370 (mmt) outliers start: 16 outliers final: 12 residues processed: 92 average time/residue: 0.0480 time to fit residues: 6.0090 Evaluate side-chains 87 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.166840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.120721 restraints weight = 4892.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.118405 restraints weight = 4418.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.119797 restraints weight = 3985.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.120178 restraints weight = 3438.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.120376 restraints weight = 3126.614| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4388 Z= 0.128 Angle : 0.631 8.269 5974 Z= 0.300 Chirality : 0.042 0.232 695 Planarity : 0.003 0.039 726 Dihedral : 6.014 74.062 617 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.41 % Allowed : 21.17 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.37), residues: 562 helix: 1.86 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.10 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 526 TYR 0.023 0.001 TYR A 590 PHE 0.010 0.001 PHE A 591 TRP 0.006 0.001 TRP A 254 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 4378) covalent geometry : angle 0.60937 / 0.29 ( 5951) SS BOND : bond 0.00164 / 0.08 ( 7) SS BOND : angle 1.99336 / 1.23 ( 14) hydrogen bonds : bond 0.03863 / 2.56 ( 263) hydrogen bonds : angle 4.04484 / 2.85 ( 777) link_BETA1-4 : bond 0.00399 / 0.21 ( 1) link_BETA1-4 : angle 4.87620 / 2.84 ( 3) link_NAG-ASN : bond 0.00287 / 0.14 ( 2) link_NAG-ASN : angle 2.56304 / 1.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8713 (tpt) cc_final: 0.8379 (tpp) REVERT: A 170 MET cc_start: 0.7650 (mmm) cc_final: 0.7244 (mmm) REVERT: A 254 TRP cc_start: 0.8130 (t-100) cc_final: 0.7590 (t60) REVERT: A 381 ILE cc_start: 0.8544 (tp) cc_final: 0.8222 (tp) outliers start: 14 outliers final: 12 residues processed: 87 average time/residue: 0.0398 time to fit residues: 4.7560 Evaluate side-chains 89 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.0770 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.166356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.120382 restraints weight = 4839.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.117936 restraints weight = 4512.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.120382 restraints weight = 4327.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.120833 restraints weight = 3293.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.120757 restraints weight = 2913.854| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4388 Z= 0.130 Angle : 0.615 8.111 5974 Z= 0.292 Chirality : 0.042 0.227 695 Planarity : 0.003 0.031 726 Dihedral : 5.832 73.111 617 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.89 % Allowed : 21.17 % Favored : 74.94 % 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: 1.18 (0.36), residues: 562 helix: 1.87 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.08 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 526 TYR 0.023 0.001 TYR A 590 PHE 0.013 0.001 PHE A 116 TRP 0.007 0.001 TRP A 254 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 4378) covalent geometry : angle 0.59709 / 0.29 ( 5951) SS BOND : bond 0.00101 / 0.05 ( 7) SS BOND : angle 1.64954 / 1.06 ( 14) hydrogen bonds : bond 0.03896 / 2.59 ( 263) hydrogen bonds : angle 4.03313 / 2.83 ( 777) link_BETA1-4 : bond 0.00412 / 0.22 ( 1) link_BETA1-4 : angle 4.55084 / 2.62 ( 3) link_NAG-ASN : bond 0.00299 / 0.15 ( 2) link_NAG-ASN : angle 2.41176 / 1.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8707 (tpt) cc_final: 0.8340 (tpp) REVERT: A 176 MET cc_start: 0.7924 (tpp) cc_final: 0.7440 (tpp) REVERT: A 254 TRP cc_start: 0.8144 (t-100) cc_final: 0.7692 (t60) REVERT: A 381 ILE cc_start: 0.8575 (tp) cc_final: 0.8250 (tp) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.0542 time to fit residues: 6.3000 Evaluate side-chains 85 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 45 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.0170 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 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 = 0.3764 r_free = 0.3764 target = 0.167997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.117605 restraints weight = 4824.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.119719 restraints weight = 3599.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.121381 restraints weight = 2984.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.122567 restraints weight = 2611.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.122567 restraints weight = 2385.688| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4388 Z= 0.123 Angle : 0.617 7.878 5974 Z= 0.296 Chirality : 0.042 0.222 695 Planarity : 0.003 0.031 726 Dihedral : 5.768 71.168 617 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.92 % Allowed : 22.38 % Favored : 74.70 % 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: 1.24 (0.36), residues: 562 helix: 1.89 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -1.00 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 526 TYR 0.024 0.002 TYR A 590 PHE 0.012 0.001 PHE A 427 TRP 0.005 0.001 TRP A 254 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 4378) covalent geometry : angle 0.60134 / 0.29 ( 5951) SS BOND : bond 0.00076 / 0.04 ( 7) SS BOND : angle 1.54887 / 1.00 ( 14) hydrogen bonds : bond 0.03807 / 2.54 ( 263) hydrogen bonds : angle 3.99921 / 2.81 ( 777) link_BETA1-4 : bond 0.00373 / 0.20 ( 1) link_BETA1-4 : angle 4.37390 / 2.53 ( 3) link_NAG-ASN : bond 0.00297 / 0.15 ( 2) link_NAG-ASN : angle 2.36297 / 1.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8619 (tpt) cc_final: 0.8299 (tpp) REVERT: A 176 MET cc_start: 0.7901 (tpp) cc_final: 0.7416 (tpp) REVERT: A 246 ARG cc_start: 0.7953 (mpt-90) cc_final: 0.7156 (ptt-90) REVERT: A 254 TRP cc_start: 0.8131 (t-100) cc_final: 0.7685 (t60) REVERT: A 381 ILE cc_start: 0.8529 (tp) cc_final: 0.8223 (tp) REVERT: A 382 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8651 (m) outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 0.0531 time to fit residues: 5.8636 Evaluate side-chains 84 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 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 = 0.3788 r_free = 0.3788 target = 0.169364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.124871 restraints weight = 4845.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.122522 restraints weight = 4320.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.123735 restraints weight = 4380.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.124695 restraints weight = 3659.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.124550 restraints weight = 3120.013| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4388 Z= 0.137 Angle : 0.630 7.705 5974 Z= 0.301 Chirality : 0.044 0.299 695 Planarity : 0.003 0.025 726 Dihedral : 5.757 71.767 617 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.68 % Allowed : 22.14 % Favored : 75.18 % 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: 1.26 (0.36), residues: 562 helix: 1.88 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -0.96 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 526 TYR 0.026 0.002 TYR A 234 PHE 0.011 0.001 PHE A 427 TRP 0.006 0.001 TRP A 254 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4378) covalent geometry : angle 0.61555 / 0.30 ( 5951) SS BOND : bond 0.00099 / 0.05 ( 7) SS BOND : angle 1.48027 / 0.95 ( 14) hydrogen bonds : bond 0.03904 / 2.61 ( 263) hydrogen bonds : angle 4.03881 / 2.83 ( 777) link_BETA1-4 : bond 0.00426 / 0.22 ( 1) link_BETA1-4 : angle 4.20890 / 2.42 ( 3) link_NAG-ASN : bond 0.00283 / 0.14 ( 2) link_NAG-ASN : angle 2.30767 / 1.58 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8728 (tpt) cc_final: 0.8366 (tpp) REVERT: A 176 MET cc_start: 0.7950 (tpp) cc_final: 0.7480 (tpp) REVERT: A 254 TRP cc_start: 0.8170 (t-100) cc_final: 0.7757 (t60) REVERT: A 381 ILE cc_start: 0.8604 (tp) cc_final: 0.8281 (tp) REVERT: A 382 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8780 (m) REVERT: A 395 TYR cc_start: 0.7055 (t80) cc_final: 0.6823 (t80) outliers start: 11 outliers final: 10 residues processed: 76 average time/residue: 0.0394 time to fit residues: 4.0578 Evaluate side-chains 80 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 43 optimal weight: 50.0000 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 30.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 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 = 0.3750 r_free = 0.3750 target = 0.166597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.122244 restraints weight = 4816.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.119331 restraints weight = 4067.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.119473 restraints weight = 3991.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.119984 restraints weight = 4077.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.120627 restraints weight = 3458.139| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4388 Z= 0.131 Angle : 0.632 8.096 5974 Z= 0.301 Chirality : 0.043 0.268 695 Planarity : 0.003 0.025 726 Dihedral : 5.709 71.890 617 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.92 % Allowed : 21.90 % Favored : 75.18 % 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: 1.32 (0.36), residues: 562 helix: 1.93 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -0.93 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 526 TYR 0.052 0.002 TYR A 234 PHE 0.011 0.001 PHE A 427 TRP 0.007 0.001 TRP A 254 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4378) covalent geometry : angle 0.61826 / 0.30 ( 5951) SS BOND : bond 0.00083 / 0.04 ( 7) SS BOND : angle 1.42625 / 0.92 ( 14) hydrogen bonds : bond 0.03881 / 2.59 ( 263) hydrogen bonds : angle 4.01366 / 2.81 ( 777) link_BETA1-4 : bond 0.00446 / 0.23 ( 1) link_BETA1-4 : angle 4.06551 / 2.34 ( 3) link_NAG-ASN : bond 0.00286 / 0.14 ( 2) link_NAG-ASN : angle 2.26513 / 1.56 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 834.61 seconds wall clock time: 15 minutes 5.15 seconds (905.15 seconds total)