Starting phenix.real_space_refine on Tue Mar 3 13:01:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uac_26420/03_2026/7uac_26420.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uac_26420/03_2026/7uac_26420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uac_26420/03_2026/7uac_26420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uac_26420/03_2026/7uac_26420.map" model { file = "/net/cci-nas-00/data/ceres_data/7uac_26420/03_2026/7uac_26420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uac_26420/03_2026/7uac_26420.cif" } resolution = 2.7 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= 0.003 sd= 0.045 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 S 21 5.16 5 C 2860 2.51 5 N 759 2.21 5 O 897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4540 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 4404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4404 Classifications: {'peptide': 546} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 528} Chain breaks: 3 Chain: "A" 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 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 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" 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 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.25, per 1000 atoms: 0.28 Number of scatterers: 4540 At special positions: 0 Unit cell: (94.34, 77.38, 92.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 21 16.00 O 897 8.00 N 759 7.00 C 2860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 107 " - pdb=" SG CYS H 259 " distance=2.03 Simple disulfide: pdb=" SG CYS H 128 " - pdb=" SG CYS H 147 " distance=2.02 Simple disulfide: pdb=" SG CYS H 269 " - pdb=" SG CYS H 277 " distance=2.03 Simple disulfide: pdb=" SG CYS H 343 " - pdb=" SG CYS H 431 " distance=2.05 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 559 " distance=2.04 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 A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " BETA1-6 " NAG C 1 " - " FUC C 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN H 140 " " NAG B 1 " - " ASN H 222 " " NAG C 1 " - " ASN H 414 " " NAG D 1 " - " ASN H 440 " Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 276.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 702 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 159 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 165 " pdb="ZN ZN H 702 " - pdb=" NE2 HIS H 155 " 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 9 sheets defined 21.8% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'H' and resid 42 through 51 Processing helix chain 'H' and resid 88 through 106 Processing helix chain 'H' and resid 149 through 161 Processing helix chain 'H' and resid 165 through 169 removed outlier: 3.606A pdb=" N SER H 168 " --> pdb=" O HIS H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 174 Processing helix chain 'H' and resid 180 through 183 Processing helix chain 'H' and resid 187 through 192 Processing helix chain 'H' and resid 232 through 238 Processing helix chain 'H' and resid 246 through 258 Processing helix chain 'H' and resid 275 through 279 Processing helix chain 'H' and resid 440 through 448 Processing helix chain 'H' and resid 516 through 520 Processing helix chain 'H' and resid 546 through 550 Processing helix chain 'H' and resid 573 through 577 Processing helix chain 'H' and resid 582 through 586 Processing helix chain 'H' and resid 597 through 600 Processing sheet with id=AA1, first strand: chain 'H' and resid 110 through 112 removed outlier: 7.939A pdb=" N PHE H 122 " --> pdb=" O PRO H 80 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE H 82 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 176 through 178 Processing sheet with id=AA3, first strand: chain 'H' and resid 265 through 269 Processing sheet with id=AA4, first strand: chain 'H' and resid 265 through 269 removed outlier: 5.664A pdb=" N LEU H 421 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS H 349 " --> pdb=" O LEU H 421 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP H 423 " --> pdb=" O PHE H 347 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE H 347 " --> pdb=" O ASP H 423 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 280 through 281 removed outlier: 6.826A pdb=" N LEU H 358 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR H 379 " --> pdb=" O LEU H 358 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL H 360 " --> pdb=" O VAL H 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 434 through 438 Processing sheet with id=AA7, first strand: chain 'H' and resid 454 through 455 Processing sheet with id=AA8, first strand: chain 'H' and resid 454 through 455 removed outlier: 3.961A pdb=" N GLY H 466 " --> pdb=" O CYS H 489 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU H 482 " --> pdb=" O GLY H 569 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 484 " --> pdb=" O TRP H 567 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 551 through 554 156 hydrogen bonds defined for protein. 375 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: 0.69 Time building geometry restraints manager: 0.44 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: 861 1.32 - 1.45: 1258 1.45 - 1.57: 2495 1.57 - 1.69: 0 1.69 - 1.82: 30 Bond restraints: 4644 Sorted by residual: bond pdb=" N PRO H 412 " pdb=" CA PRO H 412 " ideal model delta sigma weight residual 1.471 1.410 0.061 1.29e-02 6.01e+03 2.26e+01 bond pdb=" C GLN H 40 " pdb=" N LYS H 41 " ideal model delta sigma weight residual 1.331 1.403 -0.072 1.51e-02 4.39e+03 2.26e+01 bond pdb=" C GLU H 39 " pdb=" N GLN H 40 " ideal model delta sigma weight residual 1.330 1.385 -0.055 1.32e-02 5.74e+03 1.75e+01 bond pdb=" N ILE H 276 " pdb=" CA ILE H 276 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" CA SER H 168 " pdb=" CB SER H 168 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.54e-02 4.22e+03 1.40e+01 ... (remaining 4639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 4534 1.87 - 3.74: 1521 3.74 - 5.61: 202 5.61 - 7.48: 30 7.48 - 9.35: 5 Bond angle restraints: 6292 Sorted by residual: angle pdb=" CA PHE H 590 " pdb=" CB PHE H 590 " pdb=" CG PHE H 590 " ideal model delta sigma weight residual 113.80 120.35 -6.55 1.00e+00 1.00e+00 4.28e+01 angle pdb=" N GLN H 135 " pdb=" CA GLN H 135 " pdb=" C GLN H 135 " ideal model delta sigma weight residual 113.30 104.70 8.60 1.34e+00 5.57e-01 4.12e+01 angle pdb=" C PRO H 412 " pdb=" CA PRO H 412 " pdb=" CB PRO H 412 " ideal model delta sigma weight residual 112.55 121.90 -9.35 1.50e+00 4.44e-01 3.88e+01 angle pdb=" CA GLY H 138 " pdb=" C GLY H 138 " pdb=" O GLY H 138 " ideal model delta sigma weight residual 122.23 118.25 3.98 6.90e-01 2.10e+00 3.32e+01 angle pdb=" CA ASP H 134 " pdb=" CB ASP H 134 " pdb=" CG ASP H 134 " ideal model delta sigma weight residual 112.60 118.31 -5.71 1.00e+00 1.00e+00 3.26e+01 ... (remaining 6287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.46: 2693 22.46 - 44.92: 116 44.92 - 67.38: 22 67.38 - 89.84: 7 89.84 - 112.30: 22 Dihedral angle restraints: 2860 sinusoidal: 1279 harmonic: 1581 Sorted by residual: dihedral pdb=" CB CYS H 128 " pdb=" SG CYS H 128 " pdb=" SG CYS H 147 " pdb=" CB CYS H 147 " ideal model delta sinusoidal sigma weight residual 93.00 151.89 -58.89 1 1.00e+01 1.00e-02 4.64e+01 dihedral pdb=" C PRO H 412 " pdb=" N PRO H 412 " pdb=" CA PRO H 412 " pdb=" CB PRO H 412 " ideal model delta harmonic sigma weight residual -120.70 -134.70 14.00 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" CA ILE H 424 " pdb=" C ILE H 424 " pdb=" N THR H 425 " pdb=" CA THR H 425 " ideal model delta harmonic sigma weight residual 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 2857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 571 0.128 - 0.256: 109 0.256 - 0.384: 18 0.384 - 0.511: 2 0.511 - 0.639: 1 Chirality restraints: 701 Sorted by residual: chirality pdb=" C1 FUC C 4 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 4 " pdb=" O5 FUC C 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.54e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.76e+01 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 -2.26 -0.14 2.00e-02 2.50e+03 5.09e+01 ... (remaining 698 not shown) Planarity restraints: 809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.228 2.00e-02 2.50e+03 1.93e-01 4.64e+02 pdb=" C7 NAG A 1 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.155 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.326 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.218 2.00e-02 2.50e+03 1.82e-01 4.12e+02 pdb=" C7 NAG D 1 " 0.059 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.154 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.300 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.115 2.00e-02 2.50e+03 9.51e-02 1.13e+02 pdb=" C7 NAG C 1 " -0.033 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.151 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.018 2.00e-02 2.50e+03 ... (remaining 806 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 3 2.28 - 2.94: 1967 2.94 - 3.59: 5970 3.59 - 4.25: 11163 4.25 - 4.90: 18169 Nonbonded interactions: 37272 Sorted by model distance: nonbonded pdb=" OD1 ASP H 58 " pdb="ZN ZN H 702 " model vdw 1.626 2.230 nonbonded pdb=" CG ASP H 58 " pdb="ZN ZN H 702 " model vdw 2.169 2.460 nonbonded pdb=" OD2 ASP H 58 " pdb="ZN ZN H 702 " model vdw 2.250 2.230 nonbonded pdb=" OD1 ASP H 288 " pdb="CA CA H 701 " model vdw 2.332 2.510 nonbonded pdb=" OD1 ASP H 285 " pdb="CA CA H 701 " model vdw 2.343 2.510 ... (remaining 37267 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' selection = chain 'B' selection = chain 'D' } 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: 0.640 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.950 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.013 0.328 4662 Z= 0.748 Angle : 1.785 9.345 6332 Z= 1.198 Chirality : 0.109 0.639 701 Planarity : 0.015 0.193 805 Dihedral : 17.447 112.300 1829 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 11.76 % 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: -0.63 (0.33), residues: 538 helix: -0.90 (0.48), residues: 78 sheet: 0.08 (0.43), residues: 127 loop : -0.44 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 169 TYR 0.081 0.014 TYR H 119 PHE 0.060 0.011 PHE H 593 TRP 0.068 0.012 TRP H 180 HIS 0.013 0.003 HIS H 159 Details of bonding type rmsd covalent geometry : bond 0.01174 ( 4644) covalent geometry : angle 1.78574 ( 6292) SS BOND : bond 0.00963 ( 5) SS BOND : angle 1.93492 ( 10) hydrogen bonds : bond 0.17638 ( 150) hydrogen bonds : angle 7.49015 ( 375) metal coordination : bond 0.24399 ( 3) link_BETA1-4 : bond 0.00123 ( 5) link_BETA1-4 : angle 1.03884 ( 15) link_BETA1-6 : bond 0.00641 ( 1) link_BETA1-6 : angle 0.68394 ( 3) link_NAG-ASN : bond 0.00440 ( 4) link_NAG-ASN : angle 2.18404 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: H 130 SER cc_start: 0.8444 (t) cc_final: 0.8060 (m) REVERT: H 150 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7761 (ttmt) REVERT: H 154 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7768 (mt-10) REVERT: H 156 GLU cc_start: 0.8764 (mm-30) cc_final: 0.7882 (mm-30) REVERT: H 183 ILE cc_start: 0.9047 (mt) cc_final: 0.8817 (mt) REVERT: H 192 ASP cc_start: 0.7554 (m-30) cc_final: 0.7349 (m-30) REVERT: H 207 ASP cc_start: 0.7777 (t0) cc_final: 0.7274 (t0) REVERT: H 212 MET cc_start: 0.8763 (mmm) cc_final: 0.8176 (mmp) REVERT: H 225 VAL cc_start: 0.8804 (t) cc_final: 0.8522 (p) REVERT: H 244 ASP cc_start: 0.7817 (t70) cc_final: 0.7600 (t0) REVERT: H 249 ASP cc_start: 0.7590 (m-30) cc_final: 0.7367 (m-30) REVERT: H 251 GLU cc_start: 0.7637 (tt0) cc_final: 0.7378 (tt0) REVERT: H 256 MET cc_start: 0.8697 (ttp) cc_final: 0.8272 (ttt) REVERT: H 323 SER cc_start: 0.8765 (t) cc_final: 0.8346 (p) REVERT: H 326 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7084 (mt-10) REVERT: H 423 ASP cc_start: 0.8087 (m-30) cc_final: 0.7654 (m-30) REVERT: H 492 GLU cc_start: 0.7887 (pt0) cc_final: 0.7250 (tm-30) REVERT: H 525 MET cc_start: 0.7589 (mmt) cc_final: 0.7310 (mmm) REVERT: H 527 PHE cc_start: 0.8466 (p90) cc_final: 0.8030 (p90) REVERT: H 543 ILE cc_start: 0.9345 (mt) cc_final: 0.9120 (mm) REVERT: H 565 LEU cc_start: 0.9180 (tt) cc_final: 0.8928 (tm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.6209 time to fit residues: 104.2385 Evaluate side-chains 98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 40 GLN H 124 GLN H 203 ASN H 370 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.091903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081919 restraints weight = 8681.689| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.45 r_work: 0.3145 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4662 Z= 0.176 Angle : 0.730 8.767 6332 Z= 0.374 Chirality : 0.048 0.189 701 Planarity : 0.005 0.034 805 Dihedral : 14.323 107.565 796 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.07 % Allowed : 11.57 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.03 (0.34), residues: 538 helix: 0.91 (0.62), residues: 71 sheet: 0.38 (0.42), residues: 142 loop : -0.30 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 74 TYR 0.017 0.002 TYR H 113 PHE 0.017 0.002 PHE H 593 TRP 0.010 0.001 TRP H 129 HIS 0.003 0.001 HIS H 165 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 4644) covalent geometry : angle 0.71402 ( 6292) SS BOND : bond 0.00283 ( 5) SS BOND : angle 2.49432 ( 10) hydrogen bonds : bond 0.04152 ( 150) hydrogen bonds : angle 5.99529 ( 375) metal coordination : bond 0.00953 ( 3) link_BETA1-4 : bond 0.00523 ( 5) link_BETA1-4 : angle 1.44807 ( 15) link_BETA1-6 : bond 0.00379 ( 1) link_BETA1-6 : angle 2.56544 ( 3) link_NAG-ASN : bond 0.00328 ( 4) link_NAG-ASN : angle 2.09489 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.161 Fit side-chains REVERT: H 42 ASP cc_start: 0.7271 (p0) cc_final: 0.6926 (p0) REVERT: H 105 LYS cc_start: 0.8808 (mttt) cc_final: 0.8603 (mttt) REVERT: H 116 GLU cc_start: 0.7395 (mp0) cc_final: 0.7071 (mp0) REVERT: H 117 SER cc_start: 0.8304 (m) cc_final: 0.8040 (p) REVERT: H 130 SER cc_start: 0.8830 (t) cc_final: 0.8353 (m) REVERT: H 192 ASP cc_start: 0.8253 (m-30) cc_final: 0.7910 (m-30) REVERT: H 207 ASP cc_start: 0.8301 (t0) cc_final: 0.7988 (t0) REVERT: H 212 MET cc_start: 0.8898 (mmm) cc_final: 0.8654 (mmp) REVERT: H 244 ASP cc_start: 0.8404 (t70) cc_final: 0.8190 (t0) REVERT: H 249 ASP cc_start: 0.8453 (m-30) cc_final: 0.8105 (m-30) REVERT: H 251 GLU cc_start: 0.8746 (tt0) cc_final: 0.8175 (tp30) REVERT: H 252 ARG cc_start: 0.9087 (mtm-85) cc_final: 0.8727 (mtm-85) REVERT: H 284 ARG cc_start: 0.5911 (ttt180) cc_final: 0.0623 (tmt170) REVERT: H 304 LEU cc_start: 0.9343 (mt) cc_final: 0.8960 (mm) REVERT: H 319 THR cc_start: 0.8890 (p) cc_final: 0.8353 (m) REVERT: H 323 SER cc_start: 0.9062 (t) cc_final: 0.8839 (p) REVERT: H 331 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: H 385 ASP cc_start: 0.8825 (t0) cc_final: 0.8528 (t0) REVERT: H 415 SER cc_start: 0.8849 (t) cc_final: 0.8467 (p) REVERT: H 428 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8179 (mt-10) REVERT: H 483 ARG cc_start: 0.8269 (ttt-90) cc_final: 0.7932 (ttt180) REVERT: H 499 TRP cc_start: 0.8871 (m100) cc_final: 0.8557 (m100) REVERT: H 525 MET cc_start: 0.8524 (mmt) cc_final: 0.8272 (mmm) REVERT: H 543 ILE cc_start: 0.9382 (mt) cc_final: 0.9156 (mm) outliers start: 10 outliers final: 1 residues processed: 113 average time/residue: 0.5359 time to fit residues: 62.7901 Evaluate side-chains 94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 552 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN H 386 HIS H 455 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081896 restraints weight = 8606.672| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.43 r_work: 0.3138 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4662 Z= 0.149 Angle : 0.647 6.787 6332 Z= 0.334 Chirality : 0.046 0.171 701 Planarity : 0.004 0.041 805 Dihedral : 10.033 108.729 796 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.07 % Allowed : 14.88 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.09 (0.34), residues: 538 helix: 0.81 (0.60), residues: 77 sheet: 0.32 (0.42), residues: 144 loop : -0.19 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 546 TYR 0.009 0.001 TYR H 403 PHE 0.017 0.002 PHE H 593 TRP 0.008 0.001 TRP H 289 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4644) covalent geometry : angle 0.63691 ( 6292) SS BOND : bond 0.00294 ( 5) SS BOND : angle 1.31565 ( 10) hydrogen bonds : bond 0.03913 ( 150) hydrogen bonds : angle 5.56458 ( 375) metal coordination : bond 0.00982 ( 3) link_BETA1-4 : bond 0.00662 ( 5) link_BETA1-4 : angle 1.58511 ( 15) link_BETA1-6 : bond 0.00742 ( 1) link_BETA1-6 : angle 1.86057 ( 3) link_NAG-ASN : bond 0.00216 ( 4) link_NAG-ASN : angle 1.59473 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.104 Fit side-chains REVERT: H 42 ASP cc_start: 0.7246 (p0) cc_final: 0.7030 (p0) REVERT: H 116 GLU cc_start: 0.7594 (mp0) cc_final: 0.7270 (mp0) REVERT: H 130 SER cc_start: 0.8824 (t) cc_final: 0.8339 (m) REVERT: H 192 ASP cc_start: 0.8274 (m-30) cc_final: 0.7901 (m-30) REVERT: H 207 ASP cc_start: 0.8317 (t0) cc_final: 0.7927 (t0) REVERT: H 212 MET cc_start: 0.8949 (mmm) cc_final: 0.8596 (mmp) REVERT: H 238 ILE cc_start: 0.9139 (mp) cc_final: 0.8857 (mp) REVERT: H 244 ASP cc_start: 0.8461 (t70) cc_final: 0.8110 (t0) REVERT: H 249 ASP cc_start: 0.8428 (m-30) cc_final: 0.7763 (m-30) REVERT: H 284 ARG cc_start: 0.5905 (ttt180) cc_final: 0.0827 (tmt170) REVERT: H 299 GLU cc_start: 0.7917 (mp0) cc_final: 0.7690 (mp0) REVERT: H 301 ASP cc_start: 0.7936 (p0) cc_final: 0.7511 (p0) REVERT: H 319 THR cc_start: 0.8973 (p) cc_final: 0.8644 (m) REVERT: H 323 SER cc_start: 0.9042 (t) cc_final: 0.8804 (p) REVERT: H 331 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: H 385 ASP cc_start: 0.8931 (t0) cc_final: 0.8683 (t0) REVERT: H 411 ASP cc_start: 0.8183 (t0) cc_final: 0.7955 (t0) REVERT: H 415 SER cc_start: 0.8916 (t) cc_final: 0.8530 (p) REVERT: H 428 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8161 (mt-10) REVERT: H 483 ARG cc_start: 0.8167 (ttt-90) cc_final: 0.7885 (ttt180) REVERT: H 494 ASP cc_start: 0.8454 (p0) cc_final: 0.7640 (t0) REVERT: H 499 TRP cc_start: 0.8821 (m100) cc_final: 0.8394 (m100) REVERT: H 525 MET cc_start: 0.8519 (mmt) cc_final: 0.8292 (mmm) REVERT: H 543 ILE cc_start: 0.9359 (mt) cc_final: 0.9090 (mm) REVERT: H 546 ARG cc_start: 0.7870 (mtp-110) cc_final: 0.7162 (mmm160) REVERT: H 561 ARG cc_start: 0.8486 (mtt-85) cc_final: 0.8272 (mtm-85) REVERT: H 578 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8177 (ptp90) REVERT: H 584 ASN cc_start: 0.8823 (t0) cc_final: 0.8291 (t160) REVERT: H 586 ASP cc_start: 0.7587 (m-30) cc_final: 0.7238 (m-30) REVERT: H 594 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7680 (mm-30) outliers start: 10 outliers final: 4 residues processed: 111 average time/residue: 0.4674 time to fit residues: 53.8288 Evaluate side-chains 98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 578 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.0770 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN H 203 ASN H 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.080615 restraints weight = 8640.523| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.44 r_work: 0.3116 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4662 Z= 0.157 Angle : 0.603 7.504 6332 Z= 0.314 Chirality : 0.045 0.159 701 Planarity : 0.004 0.041 805 Dihedral : 8.422 94.330 796 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.89 % Allowed : 15.50 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.02 (0.35), residues: 538 helix: 0.90 (0.60), residues: 77 sheet: 0.33 (0.43), residues: 146 loop : -0.31 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 546 TYR 0.009 0.001 TYR H 403 PHE 0.020 0.002 PHE H 37 TRP 0.009 0.001 TRP H 289 HIS 0.005 0.001 HIS H 159 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 4644) covalent geometry : angle 0.59477 ( 6292) SS BOND : bond 0.00259 ( 5) SS BOND : angle 1.13651 ( 10) hydrogen bonds : bond 0.03688 ( 150) hydrogen bonds : angle 5.38809 ( 375) metal coordination : bond 0.00996 ( 3) link_BETA1-4 : bond 0.00380 ( 5) link_BETA1-4 : angle 1.45160 ( 15) link_BETA1-6 : bond 0.01083 ( 1) link_BETA1-6 : angle 2.00738 ( 3) link_NAG-ASN : bond 0.00123 ( 4) link_NAG-ASN : angle 1.39797 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.177 Fit side-chains REVERT: H 116 GLU cc_start: 0.7691 (mp0) cc_final: 0.7311 (mp0) REVERT: H 130 SER cc_start: 0.8827 (t) cc_final: 0.8344 (m) REVERT: H 192 ASP cc_start: 0.8221 (m-30) cc_final: 0.7837 (m-30) REVERT: H 207 ASP cc_start: 0.8282 (t0) cc_final: 0.7883 (t0) REVERT: H 212 MET cc_start: 0.8949 (mmm) cc_final: 0.8698 (mmp) REVERT: H 238 ILE cc_start: 0.9160 (mp) cc_final: 0.8891 (mp) REVERT: H 249 ASP cc_start: 0.8476 (m-30) cc_final: 0.7849 (m-30) REVERT: H 252 ARG cc_start: 0.9098 (mtm-85) cc_final: 0.8690 (mtm-85) REVERT: H 284 ARG cc_start: 0.6074 (ttt180) cc_final: 0.0841 (tmt170) REVERT: H 301 ASP cc_start: 0.8128 (p0) cc_final: 0.7692 (p0) REVERT: H 319 THR cc_start: 0.9112 (p) cc_final: 0.8686 (m) REVERT: H 323 SER cc_start: 0.9094 (t) cc_final: 0.8870 (p) REVERT: H 331 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: H 385 ASP cc_start: 0.8933 (t0) cc_final: 0.8681 (t0) REVERT: H 411 ASP cc_start: 0.8142 (t0) cc_final: 0.7864 (t0) REVERT: H 415 SER cc_start: 0.8933 (t) cc_final: 0.8538 (p) REVERT: H 428 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8162 (mt-10) REVERT: H 483 ARG cc_start: 0.8224 (ttt-90) cc_final: 0.7903 (ttt180) REVERT: H 494 ASP cc_start: 0.8502 (p0) cc_final: 0.8172 (p0) REVERT: H 525 MET cc_start: 0.8507 (mmt) cc_final: 0.8291 (mmm) REVERT: H 543 ILE cc_start: 0.9334 (mt) cc_final: 0.9076 (mm) REVERT: H 578 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8585 (ptp90) REVERT: H 584 ASN cc_start: 0.8816 (t0) cc_final: 0.8225 (t160) REVERT: H 585 ASP cc_start: 0.7788 (t0) cc_final: 0.7569 (t0) REVERT: H 586 ASP cc_start: 0.7505 (m-30) cc_final: 0.7164 (m-30) REVERT: H 594 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7728 (mm-30) outliers start: 14 outliers final: 5 residues processed: 115 average time/residue: 0.5275 time to fit residues: 63.0156 Evaluate side-chains 96 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 218 SER Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 578 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.0060 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN H 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.079597 restraints weight = 8568.350| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.41 r_work: 0.3105 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4662 Z= 0.177 Angle : 0.609 8.379 6332 Z= 0.314 Chirality : 0.045 0.164 701 Planarity : 0.004 0.044 805 Dihedral : 7.318 73.586 796 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.07 % Allowed : 17.56 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.23 (0.35), residues: 538 helix: 0.61 (0.57), residues: 84 sheet: 0.16 (0.42), residues: 152 loop : -0.49 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 74 TYR 0.010 0.001 TYR H 81 PHE 0.025 0.002 PHE H 37 TRP 0.011 0.001 TRP H 567 HIS 0.005 0.001 HIS H 159 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 4644) covalent geometry : angle 0.60065 ( 6292) SS BOND : bond 0.00230 ( 5) SS BOND : angle 1.05832 ( 10) hydrogen bonds : bond 0.03667 ( 150) hydrogen bonds : angle 5.34151 ( 375) metal coordination : bond 0.01106 ( 3) link_BETA1-4 : bond 0.00358 ( 5) link_BETA1-4 : angle 1.33319 ( 15) link_BETA1-6 : bond 0.01337 ( 1) link_BETA1-6 : angle 2.37479 ( 3) link_NAG-ASN : bond 0.00143 ( 4) link_NAG-ASN : angle 1.36185 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: H 106 SER cc_start: 0.8787 (t) cc_final: 0.8566 (p) REVERT: H 116 GLU cc_start: 0.7788 (mp0) cc_final: 0.7397 (mp0) REVERT: H 130 SER cc_start: 0.8814 (t) cc_final: 0.8340 (m) REVERT: H 171 ASP cc_start: 0.8333 (p0) cc_final: 0.8026 (p0) REVERT: H 192 ASP cc_start: 0.8222 (m-30) cc_final: 0.7826 (m-30) REVERT: H 207 ASP cc_start: 0.8277 (t0) cc_final: 0.7806 (t0) REVERT: H 212 MET cc_start: 0.8977 (mmm) cc_final: 0.8666 (mmp) REVERT: H 238 ILE cc_start: 0.9139 (mp) cc_final: 0.8866 (mp) REVERT: H 249 ASP cc_start: 0.8436 (m-30) cc_final: 0.7824 (m-30) REVERT: H 252 ARG cc_start: 0.9098 (mtm-85) cc_final: 0.8639 (mtm-85) REVERT: H 284 ARG cc_start: 0.6084 (ttt180) cc_final: 0.4837 (mtp180) REVERT: H 301 ASP cc_start: 0.8260 (p0) cc_final: 0.7864 (p0) REVERT: H 319 THR cc_start: 0.9109 (p) cc_final: 0.8718 (m) REVERT: H 323 SER cc_start: 0.9160 (t) cc_final: 0.8939 (p) REVERT: H 331 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: H 385 ASP cc_start: 0.8947 (t0) cc_final: 0.8713 (t0) REVERT: H 411 ASP cc_start: 0.8182 (t0) cc_final: 0.7952 (t0) REVERT: H 415 SER cc_start: 0.8905 (t) cc_final: 0.8466 (p) REVERT: H 428 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8163 (mt-10) REVERT: H 483 ARG cc_start: 0.8274 (ttt-90) cc_final: 0.8002 (ttt180) REVERT: H 521 MET cc_start: 0.8961 (mtt) cc_final: 0.8631 (mtp) REVERT: H 525 MET cc_start: 0.8485 (mmt) cc_final: 0.8285 (mmm) REVERT: H 543 ILE cc_start: 0.9321 (mt) cc_final: 0.9043 (mm) REVERT: H 578 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8577 (ptp90) REVERT: H 584 ASN cc_start: 0.8908 (t0) cc_final: 0.8334 (t160) REVERT: H 585 ASP cc_start: 0.7864 (t0) cc_final: 0.7587 (t0) REVERT: H 586 ASP cc_start: 0.7604 (m-30) cc_final: 0.7222 (m-30) REVERT: H 594 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7628 (mm-30) outliers start: 10 outliers final: 3 residues processed: 107 average time/residue: 0.4750 time to fit residues: 52.9165 Evaluate side-chains 97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 578 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN H 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079949 restraints weight = 8696.145| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.41 r_work: 0.3110 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4662 Z= 0.154 Angle : 0.617 7.949 6332 Z= 0.317 Chirality : 0.044 0.154 701 Planarity : 0.004 0.041 805 Dihedral : 6.189 51.711 796 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.07 % Allowed : 17.36 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.18 (0.35), residues: 538 helix: 0.70 (0.58), residues: 83 sheet: 0.20 (0.42), residues: 150 loop : -0.46 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 546 TYR 0.009 0.001 TYR H 81 PHE 0.027 0.002 PHE H 527 TRP 0.009 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4644) covalent geometry : angle 0.61015 ( 6292) SS BOND : bond 0.00224 ( 5) SS BOND : angle 0.91732 ( 10) hydrogen bonds : bond 0.03475 ( 150) hydrogen bonds : angle 5.29199 ( 375) metal coordination : bond 0.00883 ( 3) link_BETA1-4 : bond 0.00403 ( 5) link_BETA1-4 : angle 1.26269 ( 15) link_BETA1-6 : bond 0.01576 ( 1) link_BETA1-6 : angle 1.94261 ( 3) link_NAG-ASN : bond 0.00163 ( 4) link_NAG-ASN : angle 1.34803 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: H 106 SER cc_start: 0.8775 (t) cc_final: 0.8510 (p) REVERT: H 116 GLU cc_start: 0.7800 (mp0) cc_final: 0.7437 (mp0) REVERT: H 130 SER cc_start: 0.8816 (t) cc_final: 0.8354 (m) REVERT: H 166 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8365 (mm-30) REVERT: H 171 ASP cc_start: 0.8292 (p0) cc_final: 0.7995 (p0) REVERT: H 192 ASP cc_start: 0.8189 (m-30) cc_final: 0.7796 (m-30) REVERT: H 207 ASP cc_start: 0.8278 (t0) cc_final: 0.7815 (t0) REVERT: H 212 MET cc_start: 0.8962 (mmm) cc_final: 0.8604 (mmp) REVERT: H 238 ILE cc_start: 0.9127 (mp) cc_final: 0.8866 (mp) REVERT: H 249 ASP cc_start: 0.8446 (m-30) cc_final: 0.7837 (m-30) REVERT: H 252 ARG cc_start: 0.9033 (mtm-85) cc_final: 0.8575 (mtm-85) REVERT: H 284 ARG cc_start: 0.6079 (ttt180) cc_final: 0.0872 (tmt170) REVERT: H 301 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7904 (p0) REVERT: H 319 THR cc_start: 0.9157 (p) cc_final: 0.8692 (m) REVERT: H 323 SER cc_start: 0.9167 (t) cc_final: 0.8957 (p) REVERT: H 331 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: H 385 ASP cc_start: 0.8968 (t0) cc_final: 0.8740 (t0) REVERT: H 411 ASP cc_start: 0.8113 (t0) cc_final: 0.7886 (t0) REVERT: H 415 SER cc_start: 0.8871 (t) cc_final: 0.8422 (p) REVERT: H 428 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8160 (mt-10) REVERT: H 483 ARG cc_start: 0.8201 (ttt-90) cc_final: 0.7862 (ttt180) REVERT: H 543 ILE cc_start: 0.9317 (mt) cc_final: 0.9014 (mm) REVERT: H 574 GLN cc_start: 0.8429 (tt0) cc_final: 0.8199 (tt0) REVERT: H 578 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8576 (ptp90) REVERT: H 584 ASN cc_start: 0.8927 (t0) cc_final: 0.8341 (t160) REVERT: H 585 ASP cc_start: 0.7933 (t0) cc_final: 0.7654 (t0) REVERT: H 586 ASP cc_start: 0.7616 (m-30) cc_final: 0.7239 (m-30) REVERT: H 594 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7695 (mm-30) outliers start: 10 outliers final: 3 residues processed: 106 average time/residue: 0.5393 time to fit residues: 59.3097 Evaluate side-chains 95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 301 ASP Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 578 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN H 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.089547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.079841 restraints weight = 8587.259| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.42 r_work: 0.3104 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4662 Z= 0.150 Angle : 0.627 12.796 6332 Z= 0.319 Chirality : 0.044 0.157 701 Planarity : 0.004 0.042 805 Dihedral : 5.501 51.473 796 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.65 % Allowed : 19.21 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.12 (0.35), residues: 538 helix: 0.80 (0.59), residues: 83 sheet: 0.28 (0.42), residues: 150 loop : -0.46 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 74 TYR 0.008 0.001 TYR H 81 PHE 0.033 0.002 PHE H 527 TRP 0.016 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4644) covalent geometry : angle 0.62064 ( 6292) SS BOND : bond 0.00196 ( 5) SS BOND : angle 0.88077 ( 10) hydrogen bonds : bond 0.03368 ( 150) hydrogen bonds : angle 5.27813 ( 375) metal coordination : bond 0.00820 ( 3) link_BETA1-4 : bond 0.00392 ( 5) link_BETA1-4 : angle 1.31319 ( 15) link_BETA1-6 : bond 0.01220 ( 1) link_BETA1-6 : angle 1.48102 ( 3) link_NAG-ASN : bond 0.00235 ( 4) link_NAG-ASN : angle 1.41859 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: H 106 SER cc_start: 0.8711 (t) cc_final: 0.8401 (p) REVERT: H 116 GLU cc_start: 0.7832 (mp0) cc_final: 0.7449 (mp0) REVERT: H 130 SER cc_start: 0.8799 (t) cc_final: 0.8340 (m) REVERT: H 171 ASP cc_start: 0.8288 (p0) cc_final: 0.7981 (p0) REVERT: H 192 ASP cc_start: 0.8238 (m-30) cc_final: 0.7785 (m-30) REVERT: H 207 ASP cc_start: 0.8289 (t0) cc_final: 0.7818 (t0) REVERT: H 212 MET cc_start: 0.8964 (mmm) cc_final: 0.8657 (mmp) REVERT: H 238 ILE cc_start: 0.9094 (mp) cc_final: 0.8850 (mp) REVERT: H 249 ASP cc_start: 0.8438 (m-30) cc_final: 0.7901 (m-30) REVERT: H 252 ARG cc_start: 0.9033 (mtm-85) cc_final: 0.8776 (mtm-85) REVERT: H 280 ILE cc_start: 0.9014 (pt) cc_final: 0.8707 (pp) REVERT: H 284 ARG cc_start: 0.6106 (ttt180) cc_final: 0.0928 (tmt170) REVERT: H 301 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7956 (p0) REVERT: H 319 THR cc_start: 0.9110 (p) cc_final: 0.8708 (m) REVERT: H 323 SER cc_start: 0.9131 (t) cc_final: 0.8924 (p) REVERT: H 331 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: H 385 ASP cc_start: 0.8973 (t0) cc_final: 0.8753 (t0) REVERT: H 415 SER cc_start: 0.8834 (t) cc_final: 0.8447 (p) REVERT: H 428 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8171 (mt-10) REVERT: H 483 ARG cc_start: 0.8219 (ttt-90) cc_final: 0.7952 (ttt180) REVERT: H 525 MET cc_start: 0.8569 (mmm) cc_final: 0.8160 (mmm) REVERT: H 543 ILE cc_start: 0.9294 (mt) cc_final: 0.8979 (mm) REVERT: H 574 GLN cc_start: 0.8447 (tt0) cc_final: 0.8214 (tt0) REVERT: H 578 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8586 (ptp90) REVERT: H 584 ASN cc_start: 0.8920 (t0) cc_final: 0.8321 (t160) REVERT: H 585 ASP cc_start: 0.7947 (t0) cc_final: 0.7683 (t0) REVERT: H 586 ASP cc_start: 0.7653 (m-30) cc_final: 0.7273 (m-30) REVERT: H 594 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7670 (mm-30) outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.5292 time to fit residues: 55.0024 Evaluate side-chains 98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 234 GLU Chi-restraints excluded: chain H residue 301 ASP Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 578 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.0670 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN H 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.089072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079399 restraints weight = 8709.339| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.43 r_work: 0.3104 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4662 Z= 0.165 Angle : 0.655 11.576 6332 Z= 0.332 Chirality : 0.044 0.168 701 Planarity : 0.004 0.047 805 Dihedral : 5.316 51.451 796 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.65 % Allowed : 21.28 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.10 (0.35), residues: 538 helix: 0.82 (0.59), residues: 83 sheet: 0.30 (0.42), residues: 150 loop : -0.46 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 74 TYR 0.009 0.001 TYR H 81 PHE 0.034 0.002 PHE H 527 TRP 0.024 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4644) covalent geometry : angle 0.64999 ( 6292) SS BOND : bond 0.00192 ( 5) SS BOND : angle 0.87706 ( 10) hydrogen bonds : bond 0.03372 ( 150) hydrogen bonds : angle 5.27010 ( 375) metal coordination : bond 0.00920 ( 3) link_BETA1-4 : bond 0.00394 ( 5) link_BETA1-4 : angle 1.34050 ( 15) link_BETA1-6 : bond 0.00987 ( 1) link_BETA1-6 : angle 1.31735 ( 3) link_NAG-ASN : bond 0.00174 ( 4) link_NAG-ASN : angle 1.35243 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: H 106 SER cc_start: 0.8730 (t) cc_final: 0.8410 (p) REVERT: H 116 GLU cc_start: 0.7858 (mp0) cc_final: 0.7470 (mp0) REVERT: H 130 SER cc_start: 0.8815 (t) cc_final: 0.8348 (m) REVERT: H 171 ASP cc_start: 0.8242 (p0) cc_final: 0.7942 (p0) REVERT: H 192 ASP cc_start: 0.8237 (m-30) cc_final: 0.7775 (m-30) REVERT: H 207 ASP cc_start: 0.8279 (t0) cc_final: 0.7806 (t0) REVERT: H 212 MET cc_start: 0.8978 (mmm) cc_final: 0.8488 (mmm) REVERT: H 238 ILE cc_start: 0.9119 (mp) cc_final: 0.8893 (mp) REVERT: H 249 ASP cc_start: 0.8439 (m-30) cc_final: 0.7898 (m-30) REVERT: H 252 ARG cc_start: 0.9056 (mtm-85) cc_final: 0.8788 (mtm-85) REVERT: H 280 ILE cc_start: 0.9015 (pt) cc_final: 0.8717 (pp) REVERT: H 284 ARG cc_start: 0.6114 (ttt180) cc_final: 0.4838 (mtp180) REVERT: H 301 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7994 (p0) REVERT: H 319 THR cc_start: 0.9117 (p) cc_final: 0.8743 (m) REVERT: H 323 SER cc_start: 0.9086 (t) cc_final: 0.8827 (p) REVERT: H 331 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: H 385 ASP cc_start: 0.8976 (t0) cc_final: 0.8768 (t0) REVERT: H 411 ASP cc_start: 0.8099 (t0) cc_final: 0.7831 (t70) REVERT: H 415 SER cc_start: 0.8816 (t) cc_final: 0.8409 (p) REVERT: H 428 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8183 (mt-10) REVERT: H 483 ARG cc_start: 0.8220 (ttt-90) cc_final: 0.7953 (ttt180) REVERT: H 525 MET cc_start: 0.8612 (mmm) cc_final: 0.8244 (mmm) REVERT: H 543 ILE cc_start: 0.9281 (mt) cc_final: 0.8968 (mm) REVERT: H 574 GLN cc_start: 0.8484 (tt0) cc_final: 0.8214 (tt0) REVERT: H 578 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8134 (ptp90) REVERT: H 584 ASN cc_start: 0.8935 (t0) cc_final: 0.8326 (t160) REVERT: H 585 ASP cc_start: 0.7961 (t0) cc_final: 0.7708 (t0) REVERT: H 586 ASP cc_start: 0.7652 (m-30) cc_final: 0.7284 (m-30) REVERT: H 594 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7693 (mm-30) outliers start: 8 outliers final: 4 residues processed: 99 average time/residue: 0.5591 time to fit residues: 57.4400 Evaluate side-chains 97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 301 ASP Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 578 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.0060 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079955 restraints weight = 8661.973| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.43 r_work: 0.3113 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4662 Z= 0.137 Angle : 0.642 11.423 6332 Z= 0.326 Chirality : 0.044 0.175 701 Planarity : 0.004 0.048 805 Dihedral : 5.170 51.700 796 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.65 % Allowed : 21.07 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.02 (0.35), residues: 538 helix: 0.96 (0.59), residues: 83 sheet: 0.36 (0.42), residues: 150 loop : -0.43 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 74 TYR 0.008 0.001 TYR H 81 PHE 0.034 0.002 PHE H 527 TRP 0.026 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4644) covalent geometry : angle 0.63702 ( 6292) SS BOND : bond 0.00193 ( 5) SS BOND : angle 0.86755 ( 10) hydrogen bonds : bond 0.03213 ( 150) hydrogen bonds : angle 5.23399 ( 375) metal coordination : bond 0.00683 ( 3) link_BETA1-4 : bond 0.00383 ( 5) link_BETA1-4 : angle 1.29168 ( 15) link_BETA1-6 : bond 0.00504 ( 1) link_BETA1-6 : angle 1.09177 ( 3) link_NAG-ASN : bond 0.00160 ( 4) link_NAG-ASN : angle 1.27854 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: H 106 SER cc_start: 0.8665 (t) cc_final: 0.8304 (p) REVERT: H 116 GLU cc_start: 0.7836 (mp0) cc_final: 0.7522 (mp0) REVERT: H 130 SER cc_start: 0.8809 (t) cc_final: 0.8351 (m) REVERT: H 171 ASP cc_start: 0.8248 (p0) cc_final: 0.7953 (p0) REVERT: H 192 ASP cc_start: 0.8217 (m-30) cc_final: 0.7699 (m-30) REVERT: H 207 ASP cc_start: 0.8260 (t0) cc_final: 0.7807 (t0) REVERT: H 212 MET cc_start: 0.8942 (mmm) cc_final: 0.8421 (mmm) REVERT: H 238 ILE cc_start: 0.9064 (mp) cc_final: 0.8824 (mp) REVERT: H 249 ASP cc_start: 0.8416 (m-30) cc_final: 0.7886 (m-30) REVERT: H 252 ARG cc_start: 0.9025 (mtm-85) cc_final: 0.8788 (mtm-85) REVERT: H 280 ILE cc_start: 0.9002 (pt) cc_final: 0.8698 (pp) REVERT: H 284 ARG cc_start: 0.6145 (ttt180) cc_final: 0.0958 (tmt170) REVERT: H 301 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7987 (p0) REVERT: H 331 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: H 385 ASP cc_start: 0.8987 (t0) cc_final: 0.8771 (t0) REVERT: H 411 ASP cc_start: 0.8159 (t0) cc_final: 0.7898 (t70) REVERT: H 415 SER cc_start: 0.8795 (t) cc_final: 0.8427 (p) REVERT: H 428 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8181 (mt-10) REVERT: H 478 SER cc_start: 0.8113 (m) cc_final: 0.7545 (p) REVERT: H 525 MET cc_start: 0.8617 (mmm) cc_final: 0.8265 (mmm) REVERT: H 543 ILE cc_start: 0.9250 (mt) cc_final: 0.8941 (mm) REVERT: H 574 GLN cc_start: 0.8435 (tt0) cc_final: 0.8206 (tt0) REVERT: H 578 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8428 (ptp90) REVERT: H 584 ASN cc_start: 0.8934 (t0) cc_final: 0.8319 (t160) REVERT: H 585 ASP cc_start: 0.7899 (t0) cc_final: 0.7653 (t0) REVERT: H 586 ASP cc_start: 0.7618 (m-30) cc_final: 0.7276 (m-30) REVERT: H 594 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7696 (mm-30) outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.5433 time to fit residues: 56.4187 Evaluate side-chains 97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 301 ASP Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 578 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079120 restraints weight = 8644.438| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.41 r_work: 0.3095 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4662 Z= 0.192 Angle : 0.673 11.176 6332 Z= 0.347 Chirality : 0.045 0.157 701 Planarity : 0.004 0.050 805 Dihedral : 5.236 51.479 796 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.45 % Allowed : 20.87 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.03 (0.35), residues: 538 helix: 0.91 (0.59), residues: 83 sheet: 0.39 (0.43), residues: 150 loop : -0.45 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 483 TYR 0.010 0.001 TYR H 81 PHE 0.037 0.002 PHE H 527 TRP 0.027 0.002 TRP H 567 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 4644) covalent geometry : angle 0.66824 ( 6292) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.93208 ( 10) hydrogen bonds : bond 0.03604 ( 150) hydrogen bonds : angle 5.30279 ( 375) metal coordination : bond 0.01086 ( 3) link_BETA1-4 : bond 0.00327 ( 5) link_BETA1-4 : angle 1.34762 ( 15) link_BETA1-6 : bond 0.00439 ( 1) link_BETA1-6 : angle 1.25008 ( 3) link_NAG-ASN : bond 0.00205 ( 4) link_NAG-ASN : angle 1.32861 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: H 106 SER cc_start: 0.8728 (t) cc_final: 0.8395 (p) REVERT: H 116 GLU cc_start: 0.7858 (mp0) cc_final: 0.7558 (mp0) REVERT: H 130 SER cc_start: 0.8826 (t) cc_final: 0.8367 (m) REVERT: H 171 ASP cc_start: 0.8240 (p0) cc_final: 0.7953 (p0) REVERT: H 192 ASP cc_start: 0.8235 (m-30) cc_final: 0.7772 (m-30) REVERT: H 207 ASP cc_start: 0.8285 (t0) cc_final: 0.7818 (t0) REVERT: H 212 MET cc_start: 0.8998 (mmm) cc_final: 0.8454 (mmm) REVERT: H 238 ILE cc_start: 0.9095 (mp) cc_final: 0.8856 (mp) REVERT: H 249 ASP cc_start: 0.8441 (m-30) cc_final: 0.7916 (m-30) REVERT: H 252 ARG cc_start: 0.9078 (mtm-85) cc_final: 0.8839 (mtm-85) REVERT: H 280 ILE cc_start: 0.9009 (pt) cc_final: 0.8700 (pp) REVERT: H 284 ARG cc_start: 0.6145 (ttt180) cc_final: 0.4903 (mtp180) REVERT: H 301 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8034 (p0) REVERT: H 331 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: H 385 ASP cc_start: 0.8957 (t0) cc_final: 0.8738 (t0) REVERT: H 411 ASP cc_start: 0.8256 (t0) cc_final: 0.7983 (t70) REVERT: H 415 SER cc_start: 0.8859 (t) cc_final: 0.8477 (p) REVERT: H 428 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8176 (mt-10) REVERT: H 478 SER cc_start: 0.8177 (m) cc_final: 0.7605 (p) REVERT: H 525 MET cc_start: 0.8611 (mmm) cc_final: 0.8247 (mmm) REVERT: H 543 ILE cc_start: 0.9270 (mt) cc_final: 0.8970 (mm) REVERT: H 574 GLN cc_start: 0.8490 (tt0) cc_final: 0.8256 (tt0) REVERT: H 584 ASN cc_start: 0.8936 (t0) cc_final: 0.8328 (t160) REVERT: H 585 ASP cc_start: 0.7888 (t0) cc_final: 0.7648 (t0) REVERT: H 586 ASP cc_start: 0.7651 (m-30) cc_final: 0.7300 (m-30) REVERT: H 594 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7676 (mm-30) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 0.5647 time to fit residues: 56.2523 Evaluate side-chains 95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 301 ASP Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain H residue 552 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.089097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079518 restraints weight = 8668.941| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.42 r_work: 0.3104 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4662 Z= 0.155 Angle : 0.667 11.078 6332 Z= 0.342 Chirality : 0.044 0.174 701 Planarity : 0.004 0.046 805 Dihedral : 5.209 51.366 796 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.35 % Favored : 96.47 % Rotamer: Outliers : 1.24 % Allowed : 20.87 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.00 (0.36), residues: 538 helix: 0.99 (0.60), residues: 83 sheet: 0.46 (0.43), residues: 150 loop : -0.47 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 483 TYR 0.009 0.001 TYR H 81 PHE 0.034 0.002 PHE H 527 TRP 0.028 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4644) covalent geometry : angle 0.66258 ( 6292) SS BOND : bond 0.00195 ( 5) SS BOND : angle 0.91466 ( 10) hydrogen bonds : bond 0.03403 ( 150) hydrogen bonds : angle 5.26741 ( 375) metal coordination : bond 0.00813 ( 3) link_BETA1-4 : bond 0.00374 ( 5) link_BETA1-4 : angle 1.26983 ( 15) link_BETA1-6 : bond 0.00401 ( 1) link_BETA1-6 : angle 1.19141 ( 3) link_NAG-ASN : bond 0.00140 ( 4) link_NAG-ASN : angle 1.26190 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2122.79 seconds wall clock time: 36 minutes 48.57 seconds (2208.57 seconds total)