Starting phenix.real_space_refine on Thu Jul 2 00:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uac_26420/07_2026/7uac_26420.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uac_26420/07_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_26420/07_2026/7uac_26420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uac_26420/07_2026/7uac_26420.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uac_26420/07_2026/7uac_26420.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uac_26420/07_2026/7uac_26420.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uac_26420/07_2026/7uac_26420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uac_26420/07_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-6108/lib/python3.11/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 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 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 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 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: 0.85, per 1000 atoms: 0.19 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: 0.44 Conformation dependent library (CDL) restraints added in 125.0 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: 0.52 Time building geometry restraints manager: 0.48 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 - 17.97: 2460 17.97 - 35.94: 159 35.94 - 53.91: 26 53.91 - 71.88: 8 71.88 - 89.85: 3 Dihedral angle restraints: 2656 sinusoidal: 1075 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 2653 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.070 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:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 12.813 89.846 1625 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/Z covalent geometry : bond 0.01174 / 0.72 ( 4644) covalent geometry : angle 1.78574 / 1.20 ( 6292) SS BOND : bond 0.00963 / 0.51 ( 5) SS BOND : angle 1.93492 / 1.26 ( 10) hydrogen bonds : bond 0.17638 / 11.79 ( 150) hydrogen bonds : angle 7.49015 / 5.24 ( 375) metal coordination : bond 0.24399 / 10.22 ( 3) link_BETA1-4 : bond 0.00123 / 0.06 ( 5) link_BETA1-4 : angle 1.03884 / 0.61 ( 15) link_BETA1-6 : bond 0.00641 / 0.34 ( 1) link_BETA1-6 : angle 0.68394 / 0.42 ( 3) link_NAG-ASN : bond 0.00440 / 0.17 ( 4) link_NAG-ASN : angle 2.18404 / 1.17 ( 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 : 0.158 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: 0.5205 time to fit residues: 87.5838 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 : 0.144 ------------------------------------------------------------------------------- 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... H 40 GLN H 124 GLN H 203 ASN H 370 ASN H 386 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.091376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081609 restraints weight = 8616.256| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.42 r_work: 0.3142 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4662 Z= 0.176 Angle : 0.693 7.078 6332 Z= 0.368 Chirality : 0.046 0.177 701 Planarity : 0.004 0.035 805 Dihedral : 5.582 22.241 592 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.27 % Allowed : 11.36 % 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: 0.04 (0.34), residues: 538 helix: 0.89 (0.62), residues: 71 sheet: 0.40 (0.42), residues: 142 loop : -0.29 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 74 TYR 0.017 0.001 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 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 ( 4644) covalent geometry : angle 0.67841 / 0.36 ( 6292) SS BOND : bond 0.00245 / 0.13 ( 5) SS BOND : angle 2.73183 / 1.54 ( 10) hydrogen bonds : bond 0.04329 / 2.83 ( 150) hydrogen bonds : angle 5.95923 / 4.19 ( 375) metal coordination : bond 0.00658 / 0.26 ( 3) link_BETA1-4 : bond 0.00342 / 0.18 ( 5) link_BETA1-4 : angle 0.91915 / 0.58 ( 15) link_BETA1-6 : bond 0.00113 / 0.06 ( 1) link_BETA1-6 : angle 1.46654 / 0.82 ( 3) link_NAG-ASN : bond 0.00273 / 0.14 ( 4) link_NAG-ASN : angle 2.01096 / 1.02 ( 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 122 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: H 42 ASP cc_start: 0.7304 (p0) cc_final: 0.7020 (p0) REVERT: H 53 ASP cc_start: 0.7772 (t0) cc_final: 0.7564 (t0) REVERT: H 105 LYS cc_start: 0.8823 (mttt) cc_final: 0.8618 (mttt) REVERT: H 116 GLU cc_start: 0.7353 (mp0) cc_final: 0.7056 (mp0) REVERT: H 130 SER cc_start: 0.8808 (t) cc_final: 0.8326 (m) REVERT: H 192 ASP cc_start: 0.8217 (m-30) cc_final: 0.7871 (m-30) REVERT: H 207 ASP cc_start: 0.8317 (t0) cc_final: 0.7990 (t0) REVERT: H 212 MET cc_start: 0.8901 (mmm) cc_final: 0.8665 (mmp) REVERT: H 244 ASP cc_start: 0.8404 (t70) cc_final: 0.8194 (t0) REVERT: H 249 ASP cc_start: 0.8451 (m-30) cc_final: 0.8114 (m-30) REVERT: H 251 GLU cc_start: 0.8739 (tt0) cc_final: 0.8533 (tt0) REVERT: H 284 ARG cc_start: 0.5930 (ttt180) cc_final: 0.0617 (tmt170) REVERT: H 304 LEU cc_start: 0.9350 (mt) cc_final: 0.9002 (mm) REVERT: H 319 THR cc_start: 0.8872 (p) cc_final: 0.8364 (m) REVERT: H 329 LEU cc_start: 0.9143 (mt) cc_final: 0.8932 (mt) REVERT: H 331 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: H 385 ASP cc_start: 0.8835 (t0) cc_final: 0.8547 (t0) REVERT: H 415 SER cc_start: 0.8830 (t) cc_final: 0.8447 (p) REVERT: H 428 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8160 (mt-10) REVERT: H 483 ARG cc_start: 0.8246 (ttt-90) cc_final: 0.7916 (ttt180) REVERT: H 494 ASP cc_start: 0.8530 (p0) cc_final: 0.8321 (p0) REVERT: H 525 MET cc_start: 0.8553 (mmt) cc_final: 0.8289 (mmm) REVERT: H 543 ILE cc_start: 0.9383 (mt) cc_final: 0.9149 (mm) REVERT: H 567 TRP cc_start: 0.8727 (m-90) cc_final: 0.8473 (m-90) REVERT: H 594 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7612 (mm-30) outliers start: 11 outliers final: 1 residues processed: 115 average time/residue: 0.4236 time to fit residues: 50.6374 Evaluate side-chains 92 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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: 3.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 190 ASN H 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080954 restraints weight = 8610.262| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.41 r_work: 0.3116 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4662 Z= 0.192 Angle : 0.640 6.666 6332 Z= 0.338 Chirality : 0.046 0.172 701 Planarity : 0.004 0.037 805 Dihedral : 5.167 21.910 592 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.48 % Allowed : 14.67 % Favored : 82.85 % 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: 0.01 (0.34), residues: 538 helix: 0.85 (0.59), residues: 77 sheet: 0.46 (0.42), residues: 145 loop : -0.38 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 74 TYR 0.010 0.001 TYR H 81 PHE 0.022 0.002 PHE H 527 TRP 0.009 0.001 TRP H 129 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 4644) covalent geometry : angle 0.63185 / 0.34 ( 6292) SS BOND : bond 0.00282 / 0.13 ( 5) SS BOND : angle 1.44299 / 0.88 ( 10) hydrogen bonds : bond 0.04182 / 2.72 ( 150) hydrogen bonds : angle 5.65194 / 3.97 ( 375) metal coordination : bond 0.01331 / 0.62 ( 3) link_BETA1-4 : bond 0.00303 / 0.13 ( 5) link_BETA1-4 : angle 1.09298 / 0.71 ( 15) link_BETA1-6 : bond 0.00334 / 0.18 ( 1) link_BETA1-6 : angle 1.54889 / 0.80 ( 3) link_NAG-ASN : bond 0.00178 / 0.08 ( 4) link_NAG-ASN : angle 1.65931 / 0.85 ( 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 109 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.121 Fit side-chains REVERT: H 42 ASP cc_start: 0.7250 (p0) cc_final: 0.7016 (p0) REVERT: H 53 ASP cc_start: 0.8121 (t0) cc_final: 0.7888 (t0) REVERT: H 116 GLU cc_start: 0.7636 (mp0) cc_final: 0.7327 (mp0) REVERT: H 130 SER cc_start: 0.8831 (t) cc_final: 0.8342 (m) REVERT: H 192 ASP cc_start: 0.8278 (m-30) cc_final: 0.7916 (m-30) REVERT: H 207 ASP cc_start: 0.8348 (t0) cc_final: 0.7955 (t0) REVERT: H 212 MET cc_start: 0.8950 (mmm) cc_final: 0.8616 (mmp) REVERT: H 238 ILE cc_start: 0.9149 (mp) cc_final: 0.8869 (mp) REVERT: H 249 ASP cc_start: 0.8473 (m-30) cc_final: 0.7809 (m-30) REVERT: H 252 ARG cc_start: 0.9118 (mtm-85) cc_final: 0.8728 (mtm-85) REVERT: H 284 ARG cc_start: 0.6001 (ttt180) cc_final: 0.0795 (tmt170) REVERT: H 299 GLU cc_start: 0.7956 (mp0) cc_final: 0.7721 (mp0) REVERT: H 301 ASP cc_start: 0.8062 (p0) cc_final: 0.7680 (p0) REVERT: H 331 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8078 (pm20) REVERT: H 385 ASP cc_start: 0.8900 (t0) cc_final: 0.8658 (t0) REVERT: H 411 ASP cc_start: 0.8250 (t0) cc_final: 0.8041 (t0) REVERT: H 415 SER cc_start: 0.8979 (t) cc_final: 0.8647 (p) REVERT: H 428 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8140 (mt-10) REVERT: H 483 ARG cc_start: 0.8206 (ttt-90) cc_final: 0.7899 (ttt180) REVERT: H 489 CYS cc_start: 0.8494 (m) cc_final: 0.8287 (m) REVERT: H 494 ASP cc_start: 0.8497 (p0) cc_final: 0.8287 (p0) REVERT: H 525 MET cc_start: 0.8517 (mmt) cc_final: 0.8282 (mmm) REVERT: H 543 ILE cc_start: 0.9364 (mt) cc_final: 0.9097 (mm) REVERT: H 578 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8190 (ptp90) REVERT: H 586 ASP cc_start: 0.7577 (m-30) cc_final: 0.7309 (m-30) REVERT: H 594 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7642 (mm-30) outliers start: 12 outliers final: 4 residues processed: 106 average time/residue: 0.4576 time to fit residues: 50.4199 Evaluate side-chains 92 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3424 r_free = 0.3424 target = 0.091208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081498 restraints weight = 8616.388| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.44 r_work: 0.3139 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4662 Z= 0.126 Angle : 0.588 7.271 6332 Z= 0.310 Chirality : 0.044 0.159 701 Planarity : 0.004 0.042 805 Dihedral : 4.839 20.379 592 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.48 % Allowed : 15.29 % Favored : 82.23 % 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: 1.00 (0.60), residues: 77 sheet: 0.17 (0.42), residues: 148 loop : -0.30 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 74 TYR 0.009 0.001 TYR H 403 PHE 0.024 0.002 PHE H 527 TRP 0.009 0.001 TRP H 289 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 4644) covalent geometry : angle 0.58236 / 0.31 ( 6292) SS BOND : bond 0.00243 / 0.12 ( 5) SS BOND : angle 1.11400 / 0.75 ( 10) hydrogen bonds : bond 0.03613 / 2.33 ( 150) hydrogen bonds : angle 5.44358 / 3.82 ( 375) metal coordination : bond 0.00721 / 0.34 ( 3) link_BETA1-4 : bond 0.00398 / 0.19 ( 5) link_BETA1-4 : angle 0.99635 / 0.64 ( 15) link_BETA1-6 : bond 0.00227 / 0.12 ( 1) link_BETA1-6 : angle 1.26196 / 0.66 ( 3) link_NAG-ASN : bond 0.00169 / 0.08 ( 4) link_NAG-ASN : angle 1.46859 / 0.81 ( 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 110 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.141 Fit side-chains REVERT: H 53 ASP cc_start: 0.8063 (t0) cc_final: 0.7824 (t0) REVERT: H 105 LYS cc_start: 0.9017 (mttt) cc_final: 0.8762 (mttt) REVERT: H 116 GLU cc_start: 0.7631 (mp0) cc_final: 0.7259 (mp0) REVERT: H 130 SER cc_start: 0.8838 (t) cc_final: 0.8362 (m) REVERT: H 192 ASP cc_start: 0.8215 (m-30) cc_final: 0.7843 (m-30) REVERT: H 207 ASP cc_start: 0.8300 (t0) cc_final: 0.7910 (t0) REVERT: H 212 MET cc_start: 0.8932 (mmm) cc_final: 0.8693 (mmp) REVERT: H 238 ILE cc_start: 0.9148 (mp) cc_final: 0.8914 (mp) REVERT: H 244 ASP cc_start: 0.8544 (t0) cc_final: 0.8169 (t70) REVERT: H 249 ASP cc_start: 0.8436 (m-30) cc_final: 0.7822 (m-30) REVERT: H 251 GLU cc_start: 0.8751 (tt0) cc_final: 0.8112 (tp30) REVERT: H 252 ARG cc_start: 0.9093 (mtm-85) cc_final: 0.8697 (mtm-85) REVERT: H 284 ARG cc_start: 0.6044 (ttt180) cc_final: 0.4783 (mtp180) REVERT: H 299 GLU cc_start: 0.7975 (mp0) cc_final: 0.7720 (mp0) REVERT: H 301 ASP cc_start: 0.8079 (p0) cc_final: 0.7680 (p0) REVERT: H 331 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: H 385 ASP cc_start: 0.8941 (t0) cc_final: 0.8697 (t0) REVERT: H 411 ASP cc_start: 0.8184 (t0) cc_final: 0.7900 (t0) REVERT: H 415 SER cc_start: 0.8950 (t) cc_final: 0.8544 (p) REVERT: H 428 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8173 (mt-10) REVERT: H 483 ARG cc_start: 0.8170 (ttt-90) cc_final: 0.7861 (ttt180) REVERT: H 525 MET cc_start: 0.8503 (mmt) cc_final: 0.8239 (mmm) REVERT: H 543 ILE cc_start: 0.9317 (mt) cc_final: 0.9049 (mm) REVERT: H 578 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8157 (ptp90) REVERT: H 584 ASN cc_start: 0.8812 (t0) cc_final: 0.8235 (t160) REVERT: H 586 ASP cc_start: 0.7485 (m-30) cc_final: 0.7137 (m-30) REVERT: H 594 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7561 (mm-30) outliers start: 12 outliers final: 4 residues processed: 107 average time/residue: 0.4325 time to fit residues: 48.2121 Evaluate side-chains 89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3410 r_free = 0.3410 target = 0.090208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080627 restraints weight = 8578.064| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.42 r_work: 0.3125 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4662 Z= 0.140 Angle : 0.583 7.688 6332 Z= 0.306 Chirality : 0.044 0.155 701 Planarity : 0.004 0.042 805 Dihedral : 4.658 19.969 592 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.48 % Allowed : 16.94 % 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: -0.11 (0.35), residues: 538 helix: 0.73 (0.58), residues: 83 sheet: 0.25 (0.42), residues: 150 loop : -0.42 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 74 TYR 0.009 0.001 TYR H 81 PHE 0.030 0.002 PHE H 527 TRP 0.014 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 4644) covalent geometry : angle 0.57807 / 0.31 ( 6292) SS BOND : bond 0.00212 / 0.11 ( 5) SS BOND : angle 0.97682 / 0.67 ( 10) hydrogen bonds : bond 0.03477 / 2.23 ( 150) hydrogen bonds : angle 5.30841 / 3.71 ( 375) metal coordination : bond 0.00884 / 0.42 ( 3) link_BETA1-4 : bond 0.00319 / 0.15 ( 5) link_BETA1-4 : angle 1.02311 / 0.65 ( 15) link_BETA1-6 : bond 0.00138 / 0.07 ( 1) link_BETA1-6 : angle 1.31048 / 0.70 ( 3) link_NAG-ASN : bond 0.00100 / 0.05 ( 4) link_NAG-ASN : angle 1.35757 / 0.77 ( 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 106 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: H 53 ASP cc_start: 0.8194 (t0) cc_final: 0.7933 (t0) REVERT: H 116 GLU cc_start: 0.7739 (mp0) cc_final: 0.7354 (mp0) REVERT: H 130 SER cc_start: 0.8817 (t) cc_final: 0.8357 (m) REVERT: H 171 ASP cc_start: 0.8316 (p0) cc_final: 0.8012 (p0) REVERT: H 192 ASP cc_start: 0.8177 (m-30) cc_final: 0.7779 (m-30) REVERT: H 207 ASP cc_start: 0.8285 (t0) cc_final: 0.7884 (t0) REVERT: H 212 MET cc_start: 0.8965 (mmm) cc_final: 0.8725 (mmp) REVERT: H 238 ILE cc_start: 0.9126 (mp) cc_final: 0.8835 (mp) REVERT: H 249 ASP cc_start: 0.8432 (m-30) cc_final: 0.7828 (m-30) REVERT: H 252 ARG cc_start: 0.9084 (mtm-85) cc_final: 0.8697 (mtm-85) REVERT: H 284 ARG cc_start: 0.6058 (ttt180) cc_final: 0.0825 (tmt170) REVERT: H 331 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: H 385 ASP cc_start: 0.8967 (t0) cc_final: 0.8743 (t0) REVERT: H 411 ASP cc_start: 0.8075 (t0) cc_final: 0.7824 (t0) REVERT: H 415 SER cc_start: 0.8960 (t) cc_final: 0.8531 (p) REVERT: H 428 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8181 (mt-10) REVERT: H 483 ARG cc_start: 0.8243 (ttt-90) cc_final: 0.7976 (ttt180) REVERT: H 525 MET cc_start: 0.8514 (mmt) cc_final: 0.8268 (mmm) REVERT: H 531 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8904 (mmmm) REVERT: H 543 ILE cc_start: 0.9293 (mt) cc_final: 0.9015 (mm) REVERT: H 578 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8592 (ptp90) REVERT: H 584 ASN cc_start: 0.8782 (t0) cc_final: 0.8158 (t0) REVERT: H 594 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7577 (mm-30) outliers start: 12 outliers final: 2 residues processed: 104 average time/residue: 0.4270 time to fit residues: 46.1814 Evaluate side-chains 89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 531 LYS 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: 0.0370 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3410 r_free = 0.3410 target = 0.090205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080588 restraints weight = 8709.574| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.43 r_work: 0.3120 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4662 Z= 0.135 Angle : 0.599 8.115 6332 Z= 0.313 Chirality : 0.044 0.157 701 Planarity : 0.004 0.042 805 Dihedral : 4.591 19.414 592 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.07 % Allowed : 16.32 % 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: -0.10 (0.35), residues: 538 helix: 0.74 (0.59), residues: 83 sheet: 0.21 (0.42), residues: 150 loop : -0.37 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 74 TYR 0.008 0.001 TYR H 81 PHE 0.032 0.002 PHE H 527 TRP 0.019 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 4644) covalent geometry : angle 0.59468 / 0.31 ( 6292) SS BOND : bond 0.00205 / 0.11 ( 5) SS BOND : angle 0.89710 / 0.64 ( 10) hydrogen bonds : bond 0.03352 / 2.15 ( 150) hydrogen bonds : angle 5.19002 / 3.61 ( 375) metal coordination : bond 0.00785 / 0.37 ( 3) link_BETA1-4 : bond 0.00347 / 0.17 ( 5) link_BETA1-4 : angle 0.97863 / 0.61 ( 15) link_BETA1-6 : bond 0.00156 / 0.08 ( 1) link_BETA1-6 : angle 1.26974 / 0.68 ( 3) link_NAG-ASN : bond 0.00175 / 0.09 ( 4) link_NAG-ASN : angle 1.25501 / 0.67 ( 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 107 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: H 53 ASP cc_start: 0.8222 (t0) cc_final: 0.7938 (t0) REVERT: H 116 GLU cc_start: 0.7765 (mp0) cc_final: 0.7393 (mp0) REVERT: H 130 SER cc_start: 0.8824 (t) cc_final: 0.8364 (m) REVERT: H 166 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8371 (mm-30) REVERT: H 171 ASP cc_start: 0.8303 (p0) cc_final: 0.7991 (p0) REVERT: H 192 ASP cc_start: 0.8147 (m-30) cc_final: 0.7755 (m-30) REVERT: H 207 ASP cc_start: 0.8268 (t0) cc_final: 0.7832 (t0) REVERT: H 212 MET cc_start: 0.8949 (mmm) cc_final: 0.8676 (mmp) REVERT: H 238 ILE cc_start: 0.9080 (mp) cc_final: 0.8794 (mp) REVERT: H 249 ASP cc_start: 0.8419 (m-30) cc_final: 0.7851 (m-30) REVERT: H 252 ARG cc_start: 0.9086 (mtm-85) cc_final: 0.8628 (mtm-85) REVERT: H 284 ARG cc_start: 0.6118 (ttt180) cc_final: 0.0926 (tmt170) REVERT: H 299 GLU cc_start: 0.8269 (mp0) cc_final: 0.8007 (mp0) REVERT: H 319 THR cc_start: 0.9028 (p) cc_final: 0.8652 (m) REVERT: H 331 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: H 385 ASP cc_start: 0.8992 (t0) cc_final: 0.8785 (t0) REVERT: H 411 ASP cc_start: 0.8061 (t0) cc_final: 0.7839 (t0) REVERT: H 415 SER cc_start: 0.8931 (t) cc_final: 0.8427 (p) REVERT: H 428 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8179 (mt-10) REVERT: H 483 ARG cc_start: 0.8189 (ttt-90) cc_final: 0.7854 (ttt180) REVERT: H 525 MET cc_start: 0.8477 (mmt) cc_final: 0.8245 (mmm) REVERT: H 531 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8890 (mmmm) REVERT: H 543 ILE cc_start: 0.9277 (mt) cc_final: 0.8992 (mm) REVERT: H 574 GLN cc_start: 0.8373 (tt0) cc_final: 0.8141 (tt0) REVERT: H 578 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8586 (ptp90) REVERT: H 584 ASN cc_start: 0.8851 (t0) cc_final: 0.8426 (t0) REVERT: H 594 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7673 (mm-30) outliers start: 10 outliers final: 3 residues processed: 106 average time/residue: 0.4404 time to fit residues: 48.4527 Evaluate side-chains 94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 531 LYS 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: 0.9980 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.089432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080118 restraints weight = 8620.661| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.37 r_work: 0.3123 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4662 Z= 0.145 Angle : 0.620 8.506 6332 Z= 0.324 Chirality : 0.044 0.160 701 Planarity : 0.004 0.045 805 Dihedral : 4.541 18.792 592 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.65 % Allowed : 18.80 % Favored : 79.55 % 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: 0.73 (0.59), residues: 83 sheet: 0.21 (0.42), residues: 150 loop : -0.40 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 74 TYR 0.008 0.001 TYR H 81 PHE 0.033 0.002 PHE H 527 TRP 0.022 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 4644) covalent geometry : angle 0.61560 / 0.32 ( 6292) SS BOND : bond 0.00192 / 0.11 ( 5) SS BOND : angle 0.87058 / 0.63 ( 10) hydrogen bonds : bond 0.03343 / 2.13 ( 150) hydrogen bonds : angle 5.20122 / 3.64 ( 375) metal coordination : bond 0.00809 / 0.38 ( 3) link_BETA1-4 : bond 0.00348 / 0.17 ( 5) link_BETA1-4 : angle 0.98815 / 0.62 ( 15) link_BETA1-6 : bond 0.00156 / 0.08 ( 1) link_BETA1-6 : angle 1.33024 / 0.73 ( 3) link_NAG-ASN : bond 0.00175 / 0.07 ( 4) link_NAG-ASN : angle 1.30531 / 0.71 ( 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 99 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: H 53 ASP cc_start: 0.8254 (t0) cc_final: 0.7970 (t0) REVERT: H 116 GLU cc_start: 0.7799 (mp0) cc_final: 0.7418 (mp0) REVERT: H 130 SER cc_start: 0.8819 (t) cc_final: 0.8354 (m) REVERT: H 171 ASP cc_start: 0.8276 (p0) cc_final: 0.7957 (p0) REVERT: H 192 ASP cc_start: 0.8202 (m-30) cc_final: 0.7697 (m-30) REVERT: H 207 ASP cc_start: 0.8288 (t0) cc_final: 0.7816 (t0) REVERT: H 212 MET cc_start: 0.8972 (mmm) cc_final: 0.8579 (mmp) REVERT: H 238 ILE cc_start: 0.9080 (mp) cc_final: 0.8764 (mp) REVERT: H 249 ASP cc_start: 0.8406 (m-30) cc_final: 0.7831 (m-30) REVERT: H 252 ARG cc_start: 0.9063 (mtm-85) cc_final: 0.8654 (mtm-85) REVERT: H 284 ARG cc_start: 0.6092 (ttt180) cc_final: 0.4853 (mtp180) REVERT: H 319 THR cc_start: 0.9064 (p) cc_final: 0.8698 (m) REVERT: H 385 ASP cc_start: 0.9001 (t0) cc_final: 0.8790 (t0) REVERT: H 411 ASP cc_start: 0.7969 (t0) cc_final: 0.7753 (t0) REVERT: H 415 SER cc_start: 0.8904 (t) cc_final: 0.8432 (p) REVERT: H 428 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8175 (mt-10) REVERT: H 483 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7851 (ttt180) REVERT: H 525 MET cc_start: 0.8467 (mmt) cc_final: 0.8240 (mmm) REVERT: H 543 ILE cc_start: 0.9262 (mt) cc_final: 0.8944 (mm) REVERT: H 574 GLN cc_start: 0.8382 (tt0) cc_final: 0.8142 (tt0) REVERT: H 578 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8585 (ptp90) REVERT: H 584 ASN cc_start: 0.8887 (t0) cc_final: 0.8482 (t0) REVERT: H 594 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7671 (mm-30) outliers start: 8 outliers final: 6 residues processed: 98 average time/residue: 0.4425 time to fit residues: 45.1195 Evaluate side-chains 93 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 329 LEU 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: 1.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.080369 restraints weight = 8683.422| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.44 r_work: 0.3114 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4253 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= 0.138 Angle : 0.628 9.695 6332 Z= 0.327 Chirality : 0.044 0.155 701 Planarity : 0.004 0.050 805 Dihedral : 4.512 18.888 592 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.86 % Allowed : 20.04 % Favored : 78.10 % 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: -0.07 (0.35), residues: 538 helix: 0.82 (0.59), residues: 83 sheet: 0.30 (0.42), residues: 150 loop : -0.41 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 74 TYR 0.008 0.001 TYR H 81 PHE 0.035 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/Z covalent geometry : bond 0.00322 / 0.14 ( 4644) covalent geometry : angle 0.62474 / 0.33 ( 6292) SS BOND : bond 0.00205 / 0.11 ( 5) SS BOND : angle 0.87571 / 0.62 ( 10) hydrogen bonds : bond 0.03282 / 2.10 ( 150) hydrogen bonds : angle 5.21598 / 3.65 ( 375) metal coordination : bond 0.00706 / 0.33 ( 3) link_BETA1-4 : bond 0.00324 / 0.15 ( 5) link_BETA1-4 : angle 0.95976 / 0.60 ( 15) link_BETA1-6 : bond 0.00221 / 0.12 ( 1) link_BETA1-6 : angle 1.35838 / 0.73 ( 3) link_NAG-ASN : bond 0.00115 / 0.06 ( 4) link_NAG-ASN : angle 1.22336 / 0.67 ( 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 99 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: H 53 ASP cc_start: 0.8313 (t0) cc_final: 0.8011 (t0) REVERT: H 106 SER cc_start: 0.8608 (t) cc_final: 0.8314 (p) REVERT: H 116 GLU cc_start: 0.7819 (mp0) cc_final: 0.7429 (mp0) REVERT: H 130 SER cc_start: 0.8819 (t) cc_final: 0.8371 (m) REVERT: H 171 ASP cc_start: 0.8287 (p0) cc_final: 0.7971 (p0) REVERT: H 192 ASP cc_start: 0.8192 (m-30) cc_final: 0.7682 (m-30) REVERT: H 207 ASP cc_start: 0.8285 (t0) cc_final: 0.7908 (t0) REVERT: H 212 MET cc_start: 0.8975 (mmm) cc_final: 0.8477 (mmm) REVERT: H 238 ILE cc_start: 0.9081 (mp) cc_final: 0.8816 (mp) REVERT: H 249 ASP cc_start: 0.8389 (m-30) cc_final: 0.7863 (m-30) REVERT: H 252 ARG cc_start: 0.9076 (mtm-85) cc_final: 0.8643 (mtm-85) REVERT: H 284 ARG cc_start: 0.6071 (ttt180) cc_final: 0.4796 (mtp180) REVERT: H 385 ASP cc_start: 0.8998 (t0) cc_final: 0.8777 (t0) REVERT: H 411 ASP cc_start: 0.7973 (t0) cc_final: 0.7747 (t0) REVERT: H 415 SER cc_start: 0.8889 (t) cc_final: 0.8471 (p) REVERT: H 428 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8199 (mt-10) REVERT: H 483 ARG cc_start: 0.8189 (ttt-90) cc_final: 0.7913 (ttt180) REVERT: H 525 MET cc_start: 0.8480 (mmt) cc_final: 0.8252 (mmm) REVERT: H 543 ILE cc_start: 0.9243 (mt) cc_final: 0.8932 (mm) REVERT: H 574 GLN cc_start: 0.8402 (tt0) cc_final: 0.8159 (tt0) REVERT: H 584 ASN cc_start: 0.8915 (t0) cc_final: 0.8430 (t0) REVERT: H 594 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7675 (mm-30) outliers start: 9 outliers final: 7 residues processed: 97 average time/residue: 0.4388 time to fit residues: 44.1684 Evaluate side-chains 94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 329 LEU Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 552 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.0270 chunk 50 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 0.0170 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.090504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080875 restraints weight = 8582.504| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.41 r_work: 0.3129 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4662 Z= 0.127 Angle : 0.659 12.675 6332 Z= 0.336 Chirality : 0.044 0.158 701 Planarity : 0.004 0.048 805 Dihedral : 4.515 19.883 592 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % 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: -0.01 (0.36), residues: 538 helix: 0.91 (0.60), residues: 83 sheet: 0.34 (0.42), residues: 150 loop : -0.40 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 578 TYR 0.008 0.001 TYR H 81 PHE 0.035 0.002 PHE H 527 TRP 0.023 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4644) covalent geometry : angle 0.65602 / 0.34 ( 6292) SS BOND : bond 0.00179 / 0.10 ( 5) SS BOND : angle 0.83983 / 0.61 ( 10) hydrogen bonds : bond 0.03255 / 2.05 ( 150) hydrogen bonds : angle 5.16122 / 3.62 ( 375) metal coordination : bond 0.00547 / 0.26 ( 3) link_BETA1-4 : bond 0.00376 / 0.19 ( 5) link_BETA1-4 : angle 0.96204 / 0.59 ( 15) link_BETA1-6 : bond 0.00197 / 0.10 ( 1) link_BETA1-6 : angle 1.28519 / 0.70 ( 3) link_NAG-ASN : bond 0.00151 / 0.07 ( 4) link_NAG-ASN : angle 1.21217 / 0.67 ( 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: 6 poor density : 97 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: H 53 ASP cc_start: 0.8294 (t0) cc_final: 0.8008 (t0) REVERT: H 106 SER cc_start: 0.8602 (t) cc_final: 0.8295 (p) REVERT: H 116 GLU cc_start: 0.7834 (mp0) cc_final: 0.7437 (mp0) REVERT: H 130 SER cc_start: 0.8806 (t) cc_final: 0.8360 (m) REVERT: H 171 ASP cc_start: 0.8247 (p0) cc_final: 0.7915 (p0) REVERT: H 192 ASP cc_start: 0.8192 (m-30) cc_final: 0.7670 (m-30) REVERT: H 207 ASP cc_start: 0.8243 (t0) cc_final: 0.7801 (t0) REVERT: H 212 MET cc_start: 0.8967 (mmm) cc_final: 0.8445 (mmm) REVERT: H 249 ASP cc_start: 0.8385 (m-30) cc_final: 0.7853 (m-30) REVERT: H 252 ARG cc_start: 0.9031 (mtm-85) cc_final: 0.8617 (mtm-85) REVERT: H 284 ARG cc_start: 0.6177 (ttt180) cc_final: 0.1115 (tmt170) REVERT: H 319 THR cc_start: 0.9046 (p) cc_final: 0.8705 (m) REVERT: H 331 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: H 385 ASP cc_start: 0.8993 (t0) cc_final: 0.8782 (t0) REVERT: H 411 ASP cc_start: 0.7938 (t0) cc_final: 0.7718 (t0) REVERT: H 415 SER cc_start: 0.8872 (t) cc_final: 0.8356 (p) REVERT: H 428 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8151 (mt-10) REVERT: H 447 ASN cc_start: 0.8954 (m-40) cc_final: 0.8570 (m-40) REVERT: H 483 ARG cc_start: 0.8173 (ttt-90) cc_final: 0.7900 (ttt180) REVERT: H 502 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7607 (tm-30) REVERT: H 525 MET cc_start: 0.8460 (mmt) cc_final: 0.8241 (mmm) REVERT: H 543 ILE cc_start: 0.9225 (mt) cc_final: 0.8895 (mm) REVERT: H 574 GLN cc_start: 0.8392 (tt0) cc_final: 0.8138 (tt0) REVERT: H 584 ASN cc_start: 0.8886 (t0) cc_final: 0.8395 (t0) REVERT: H 594 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7674 (mm-30) outliers start: 6 outliers final: 5 residues processed: 102 average time/residue: 0.3752 time to fit residues: 39.9182 Evaluate side-chains 100 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.097 ------------------------------------------------------------------------------- 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 329 LEU Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR 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 39 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.080217 restraints weight = 8550.743| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.41 r_work: 0.3119 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4662 Z= 0.145 Angle : 0.674 12.400 6332 Z= 0.346 Chirality : 0.044 0.159 701 Planarity : 0.004 0.051 805 Dihedral : 4.609 23.837 592 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: -0.01 (0.36), residues: 538 helix: 0.92 (0.60), residues: 83 sheet: 0.37 (0.43), residues: 150 loop : -0.42 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 578 TYR 0.008 0.001 TYR H 81 PHE 0.037 0.002 PHE H 527 TRP 0.025 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 4644) covalent geometry : angle 0.67081 / 0.35 ( 6292) SS BOND : bond 0.00170 / 0.10 ( 5) SS BOND : angle 0.88533 / 0.63 ( 10) hydrogen bonds : bond 0.03289 / 2.09 ( 150) hydrogen bonds : angle 5.20017 / 3.64 ( 375) metal coordination : bond 0.00726 / 0.34 ( 3) link_BETA1-4 : bond 0.00352 / 0.17 ( 5) link_BETA1-4 : angle 1.00034 / 0.62 ( 15) link_BETA1-6 : bond 0.00140 / 0.07 ( 1) link_BETA1-6 : angle 1.33636 / 0.73 ( 3) link_NAG-ASN : bond 0.00113 / 0.05 ( 4) link_NAG-ASN : angle 1.23164 / 0.67 ( 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 104 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: H 53 ASP cc_start: 0.8320 (t0) cc_final: 0.8028 (t0) REVERT: H 106 SER cc_start: 0.8642 (t) cc_final: 0.8297 (p) REVERT: H 116 GLU cc_start: 0.7805 (mp0) cc_final: 0.7408 (mp0) REVERT: H 130 SER cc_start: 0.8809 (t) cc_final: 0.8357 (m) REVERT: H 171 ASP cc_start: 0.8248 (p0) cc_final: 0.7922 (p0) REVERT: H 183 ILE cc_start: 0.8813 (mm) cc_final: 0.8525 (tt) REVERT: H 192 ASP cc_start: 0.8180 (m-30) cc_final: 0.7635 (m-30) REVERT: H 207 ASP cc_start: 0.8265 (t0) cc_final: 0.7930 (t0) REVERT: H 212 MET cc_start: 0.8995 (mmm) cc_final: 0.8532 (mmm) REVERT: H 249 ASP cc_start: 0.8390 (m-30) cc_final: 0.7863 (m-30) REVERT: H 252 ARG cc_start: 0.9034 (mtm-85) cc_final: 0.8626 (mtm-85) REVERT: H 284 ARG cc_start: 0.6116 (ttt180) cc_final: 0.4886 (mtp180) REVERT: H 319 THR cc_start: 0.9087 (p) cc_final: 0.8760 (m) REVERT: H 331 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: H 385 ASP cc_start: 0.8994 (t0) cc_final: 0.8790 (t0) REVERT: H 411 ASP cc_start: 0.7961 (t0) cc_final: 0.7722 (t0) REVERT: H 415 SER cc_start: 0.8878 (t) cc_final: 0.8346 (p) REVERT: H 428 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8165 (mt-10) REVERT: H 446 GLU cc_start: 0.8193 (pp20) cc_final: 0.7890 (pp20) REVERT: H 478 SER cc_start: 0.8067 (m) cc_final: 0.7483 (p) REVERT: H 502 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7571 (tm-30) REVERT: H 525 MET cc_start: 0.8512 (mmt) cc_final: 0.8278 (mmm) REVERT: H 543 ILE cc_start: 0.9228 (mt) cc_final: 0.8908 (mm) REVERT: H 574 GLN cc_start: 0.8425 (tt0) cc_final: 0.8184 (tt0) REVERT: H 584 ASN cc_start: 0.8924 (t0) cc_final: 0.8347 (t0) REVERT: H 594 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7682 (mm-30) outliers start: 7 outliers final: 5 residues processed: 102 average time/residue: 0.4071 time to fit residues: 43.2685 Evaluate side-chains 99 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 329 LEU Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 425 THR 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: 0.0070 chunk 49 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079523 restraints weight = 8599.906| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.38 r_work: 0.3114 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4405 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= 0.156 Angle : 0.683 12.171 6332 Z= 0.348 Chirality : 0.044 0.150 701 Planarity : 0.004 0.046 805 Dihedral : 4.577 21.030 592 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.28 % Favored : 95.54 % Rotamer: Outliers : 1.24 % Allowed : 21.28 % Favored : 77.48 % 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: 0.96 (0.60), residues: 83 sheet: 0.39 (0.43), residues: 150 loop : -0.43 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 483 TYR 0.009 0.001 TYR H 81 PHE 0.036 0.002 PHE H 527 TRP 0.023 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 4644) covalent geometry : angle 0.67943 / 0.35 ( 6292) SS BOND : bond 0.00184 / 0.10 ( 5) SS BOND : angle 0.93479 / 0.66 ( 10) hydrogen bonds : bond 0.03350 / 2.13 ( 150) hydrogen bonds : angle 5.25017 / 3.69 ( 375) metal coordination : bond 0.00853 / 0.40 ( 3) link_BETA1-4 : bond 0.00324 / 0.16 ( 5) link_BETA1-4 : angle 1.00648 / 0.63 ( 15) link_BETA1-6 : bond 0.00152 / 0.08 ( 1) link_BETA1-6 : angle 1.40642 / 0.77 ( 3) link_NAG-ASN : bond 0.00099 / 0.04 ( 4) link_NAG-ASN : angle 1.21964 / 0.66 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1693.68 seconds wall clock time: 29 minutes 30.27 seconds (1770.27 seconds total)