Starting phenix.real_space_refine on Thu Jul 24 00:20:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uac_26420/07_2025/7uac_26420.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uac_26420/07_2025/7uac_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_2025/7uac_26420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uac_26420/07_2025/7uac_26420.map" model { file = "/net/cci-nas-00/data/ceres_data/7uac_26420/07_2025/7uac_26420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uac_26420/07_2025/7uac_26420.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.58, per 1000 atoms: 0.79 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: 1.44 Conformation dependent library (CDL) restraints added in 571.0 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: 0.58 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: 1.30 Time building geometry restraints manager: 1.68 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: 0.570 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.950 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:14.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.068 0.012 TRP H 180 HIS 0.013 0.003 HIS H 159 PHE 0.060 0.011 PHE H 593 TYR 0.081 0.014 TYR H 119 ARG 0.007 0.001 ARG H 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 4) link_NAG-ASN : angle 2.18404 ( 12) link_BETA1-4 : bond 0.00123 ( 5) link_BETA1-4 : angle 1.03884 ( 15) hydrogen bonds : bond 0.17638 ( 150) hydrogen bonds : angle 7.49015 ( 375) link_BETA1-6 : bond 0.00641 ( 1) link_BETA1-6 : angle 0.68394 ( 3) metal coordination : bond 0.24399 ( 3) SS BOND : bond 0.00963 ( 5) SS BOND : angle 1.93492 ( 10) covalent geometry : bond 0.01174 ( 4644) covalent geometry : angle 1.78574 ( 6292) *********************** 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 : 0.482 Fit side-chains revert: symmetry clash REVERT: H 130 SER cc_start: 0.8444 (t) cc_final: 0.8059 (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: 0.7589 (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: 0.8696 (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: 0.7670 (mt-10) cc_final: 0.7084 (mt-10) REVERT: H 423 ASP cc_start: 0.8088 (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: 1.2700 time to fit residues: 213.8034 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 : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.091533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081852 restraints weight = 8484.180| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.39 r_work: 0.3148 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4662 Z= 0.174 Angle : 0.729 8.559 6332 Z= 0.375 Chirality : 0.049 0.196 701 Planarity : 0.004 0.035 805 Dihedral : 14.534 108.004 796 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.48 % Allowed : 11.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.33), residues: 538 helix: 0.90 (0.62), residues: 71 sheet: 0.42 (0.42), residues: 141 loop : -0.34 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 129 HIS 0.003 0.001 HIS H 155 PHE 0.016 0.002 PHE H 593 TYR 0.017 0.002 TYR H 113 ARG 0.007 0.001 ARG H 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 4) link_NAG-ASN : angle 2.07098 ( 12) link_BETA1-4 : bond 0.00580 ( 5) link_BETA1-4 : angle 1.45983 ( 15) hydrogen bonds : bond 0.04220 ( 150) hydrogen bonds : angle 6.01498 ( 375) link_BETA1-6 : bond 0.00456 ( 1) link_BETA1-6 : angle 2.55687 ( 3) metal coordination : bond 0.00418 ( 3) SS BOND : bond 0.00259 ( 5) SS BOND : angle 2.63324 ( 10) covalent geometry : bond 0.00400 ( 4644) covalent geometry : angle 0.71282 ( 6292) *********************** 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: 12 poor density : 110 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: H 42 ASP cc_start: 0.7291 (p0) cc_final: 0.6924 (p0) REVERT: H 105 LYS cc_start: 0.8820 (mttt) cc_final: 0.8614 (mttt) REVERT: H 116 GLU cc_start: 0.7370 (mp0) cc_final: 0.7015 (mp0) REVERT: H 117 SER cc_start: 0.8294 (m) cc_final: 0.8027 (p) REVERT: H 130 SER cc_start: 0.8822 (t) cc_final: 0.8331 (m) REVERT: H 192 ASP cc_start: 0.8215 (m-30) cc_final: 0.7871 (m-30) REVERT: H 207 ASP cc_start: 0.8303 (t0) cc_final: 0.7985 (t0) REVERT: H 212 MET cc_start: 0.8893 (mmm) cc_final: 0.8641 (mmp) REVERT: H 238 ILE cc_start: 0.9067 (mp) cc_final: 0.8857 (mp) REVERT: H 244 ASP cc_start: 0.8408 (t70) cc_final: 0.8183 (t0) REVERT: H 249 ASP cc_start: 0.8441 (m-30) cc_final: 0.8101 (m-30) REVERT: H 251 GLU cc_start: 0.8714 (tt0) cc_final: 0.8205 (tp30) REVERT: H 284 ARG cc_start: 0.5901 (ttt180) cc_final: 0.0618 (tmt170) REVERT: H 304 LEU cc_start: 0.9349 (mt) cc_final: 0.8950 (mm) REVERT: H 319 THR cc_start: 0.8862 (p) cc_final: 0.8567 (m) REVERT: H 329 LEU cc_start: 0.9140 (mt) cc_final: 0.8933 (mt) REVERT: H 331 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: H 385 ASP cc_start: 0.8815 (t0) cc_final: 0.8518 (t0) REVERT: H 415 SER cc_start: 0.8829 (t) cc_final: 0.8450 (p) REVERT: H 428 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8140 (mt-10) REVERT: H 483 ARG cc_start: 0.8238 (ttt-90) cc_final: 0.7912 (ttt180) REVERT: H 499 TRP cc_start: 0.8858 (m100) cc_final: 0.8544 (m100) REVERT: H 525 MET cc_start: 0.8497 (mmt) cc_final: 0.8244 (mmm) REVERT: H 543 ILE cc_start: 0.9382 (mt) cc_final: 0.9149 (mm) outliers start: 12 outliers final: 2 residues processed: 114 average time/residue: 1.1373 time to fit residues: 134.6374 Evaluate side-chains 94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 368 THR 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 15 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.092128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082383 restraints weight = 8577.495| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.43 r_work: 0.3150 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4662 Z= 0.145 Angle : 0.649 6.785 6332 Z= 0.334 Chirality : 0.046 0.168 701 Planarity : 0.004 0.040 805 Dihedral : 10.267 108.513 796 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.07 % Allowed : 15.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.34), residues: 538 helix: 0.87 (0.61), residues: 77 sheet: 0.49 (0.42), residues: 143 loop : -0.27 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 289 HIS 0.005 0.001 HIS H 155 PHE 0.023 0.002 PHE H 527 TYR 0.009 0.001 TYR H 403 ARG 0.009 0.001 ARG H 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 4) link_NAG-ASN : angle 1.61724 ( 12) link_BETA1-4 : bond 0.00373 ( 5) link_BETA1-4 : angle 1.44481 ( 15) hydrogen bonds : bond 0.03923 ( 150) hydrogen bonds : angle 5.61187 ( 375) link_BETA1-6 : bond 0.01243 ( 1) link_BETA1-6 : angle 2.00814 ( 3) metal coordination : bond 0.00981 ( 3) SS BOND : bond 0.00301 ( 5) SS BOND : angle 1.36346 ( 10) covalent geometry : bond 0.00328 ( 4644) covalent geometry : angle 0.64001 ( 6292) *********************** 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 112 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.512 Fit side-chains REVERT: H 42 ASP cc_start: 0.7227 (p0) cc_final: 0.7023 (p0) REVERT: H 116 GLU cc_start: 0.7567 (mp0) cc_final: 0.7229 (mp0) REVERT: H 130 SER cc_start: 0.8821 (t) cc_final: 0.8337 (m) REVERT: H 192 ASP cc_start: 0.8232 (m-30) cc_final: 0.7864 (m-30) REVERT: H 207 ASP cc_start: 0.8305 (t0) cc_final: 0.7892 (t0) REVERT: H 212 MET cc_start: 0.8926 (mmm) cc_final: 0.8599 (mmp) REVERT: H 225 VAL cc_start: 0.9113 (t) cc_final: 0.8913 (m) REVERT: H 238 ILE cc_start: 0.9157 (mp) cc_final: 0.8942 (mp) REVERT: H 244 ASP cc_start: 0.8427 (t70) cc_final: 0.8107 (t0) REVERT: H 249 ASP cc_start: 0.8455 (m-30) cc_final: 0.7795 (m-30) REVERT: H 252 ARG cc_start: 0.9108 (mtm-85) cc_final: 0.8675 (mtm-85) REVERT: H 284 ARG cc_start: 0.5888 (ttt180) cc_final: 0.0663 (tmt170) REVERT: H 301 ASP cc_start: 0.7912 (p0) cc_final: 0.7481 (p0) REVERT: H 319 THR cc_start: 0.8954 (p) cc_final: 0.8390 (m) REVERT: H 331 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: H 385 ASP cc_start: 0.8904 (t0) cc_final: 0.8672 (t0) REVERT: H 411 ASP cc_start: 0.8130 (t0) cc_final: 0.7892 (t0) REVERT: H 415 SER cc_start: 0.8891 (t) cc_final: 0.8422 (p) REVERT: H 428 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8154 (mt-10) REVERT: H 483 ARG cc_start: 0.8175 (ttt-90) cc_final: 0.7910 (ttt180) REVERT: H 489 CYS cc_start: 0.8533 (m) cc_final: 0.8325 (m) REVERT: H 494 ASP cc_start: 0.8467 (p0) cc_final: 0.7634 (t0) REVERT: H 499 TRP cc_start: 0.8826 (m100) cc_final: 0.8399 (m100) REVERT: H 525 MET cc_start: 0.8518 (mmt) cc_final: 0.8291 (mmm) REVERT: H 543 ILE cc_start: 0.9364 (mt) cc_final: 0.9097 (mm) REVERT: H 546 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7173 (mmm160) REVERT: H 578 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8226 (ptp90) REVERT: H 586 ASP cc_start: 0.7583 (m-30) cc_final: 0.7307 (m-30) outliers start: 10 outliers final: 4 residues processed: 110 average time/residue: 1.0652 time to fit residues: 122.0573 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 : 0.529 ------------------------------------------------------------------------------- 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 368 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.091143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081523 restraints weight = 8665.384| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.44 r_work: 0.3135 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3774 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= 0.133 Angle : 0.606 7.456 6332 Z= 0.314 Chirality : 0.045 0.162 701 Planarity : 0.004 0.042 805 Dihedral : 8.520 95.799 796 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.89 % Allowed : 15.91 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.35), residues: 538 helix: 0.91 (0.60), residues: 77 sheet: 0.34 (0.42), residues: 146 loop : -0.28 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 289 HIS 0.005 0.001 HIS H 155 PHE 0.029 0.002 PHE H 527 TYR 0.009 0.001 TYR H 403 ARG 0.006 0.001 ARG H 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 4) link_NAG-ASN : angle 1.41182 ( 12) link_BETA1-4 : bond 0.00369 ( 5) link_BETA1-4 : angle 1.37163 ( 15) hydrogen bonds : bond 0.03582 ( 150) hydrogen bonds : angle 5.40307 ( 375) link_BETA1-6 : bond 0.01132 ( 1) link_BETA1-6 : angle 1.97267 ( 3) metal coordination : bond 0.00770 ( 3) SS BOND : bond 0.00227 ( 5) SS BOND : angle 1.07095 ( 10) covalent geometry : bond 0.00300 ( 4644) covalent geometry : angle 0.59838 ( 6292) *********************** 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 114 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.524 Fit side-chains REVERT: H 116 GLU cc_start: 0.7669 (mp0) cc_final: 0.7288 (mp0) REVERT: H 130 SER cc_start: 0.8832 (t) cc_final: 0.8360 (m) REVERT: H 192 ASP cc_start: 0.8231 (m-30) cc_final: 0.7858 (m-30) REVERT: H 207 ASP cc_start: 0.8286 (t0) cc_final: 0.7888 (t0) REVERT: H 212 MET cc_start: 0.8927 (mmm) cc_final: 0.8538 (mmp) REVERT: H 249 ASP cc_start: 0.8472 (m-30) cc_final: 0.7851 (m-30) REVERT: H 251 GLU cc_start: 0.8773 (tt0) cc_final: 0.8133 (tp30) REVERT: H 252 ARG cc_start: 0.9072 (mtm-85) cc_final: 0.8689 (mtm-85) REVERT: H 284 ARG cc_start: 0.6051 (ttt180) cc_final: 0.4779 (mtp180) REVERT: H 301 ASP cc_start: 0.8043 (p0) cc_final: 0.7609 (p0) REVERT: H 319 THR cc_start: 0.9016 (p) cc_final: 0.8588 (p) REVERT: H 331 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: H 385 ASP cc_start: 0.8952 (t0) cc_final: 0.8698 (t0) REVERT: H 411 ASP cc_start: 0.8165 (t0) cc_final: 0.7852 (t0) REVERT: H 415 SER cc_start: 0.8920 (t) cc_final: 0.8421 (p) REVERT: H 423 ASP cc_start: 0.8579 (m-30) cc_final: 0.8224 (m-30) REVERT: H 425 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8387 (p) REVERT: H 428 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8206 (mt-10) REVERT: H 483 ARG cc_start: 0.8189 (ttt-90) cc_final: 0.7875 (ttt180) REVERT: H 489 CYS cc_start: 0.8553 (m) cc_final: 0.8241 (p) REVERT: H 494 ASP cc_start: 0.8499 (p0) cc_final: 0.8168 (p0) REVERT: H 525 MET cc_start: 0.8521 (mmt) cc_final: 0.8252 (mmm) REVERT: H 543 ILE cc_start: 0.9339 (mt) cc_final: 0.9076 (mm) REVERT: H 578 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8208 (ptp90) REVERT: H 584 ASN cc_start: 0.8807 (t0) cc_final: 0.8202 (t160) REVERT: H 585 ASP cc_start: 0.7769 (t0) cc_final: 0.7558 (t0) REVERT: H 586 ASP cc_start: 0.7461 (m-30) cc_final: 0.7096 (m-30) outliers start: 14 outliers final: 2 residues processed: 110 average time/residue: 1.0198 time to fit residues: 117.0281 Evaluate side-chains 96 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.090225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.080661 restraints weight = 8725.710| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.43 r_work: 0.3118 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3986 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= 0.154 Angle : 0.607 8.185 6332 Z= 0.313 Chirality : 0.045 0.158 701 Planarity : 0.004 0.042 805 Dihedral : 7.512 79.502 796 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.27 % Allowed : 17.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.35), residues: 538 helix: 0.67 (0.58), residues: 84 sheet: 0.25 (0.42), residues: 152 loop : -0.49 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.028 0.002 PHE H 527 TYR 0.009 0.001 TYR H 81 ARG 0.006 0.001 ARG H 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 4) link_NAG-ASN : angle 1.34988 ( 12) link_BETA1-4 : bond 0.00336 ( 5) link_BETA1-4 : angle 1.30375 ( 15) hydrogen bonds : bond 0.03580 ( 150) hydrogen bonds : angle 5.39877 ( 375) link_BETA1-6 : bond 0.01268 ( 1) link_BETA1-6 : angle 2.33881 ( 3) metal coordination : bond 0.00949 ( 3) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.98641 ( 10) covalent geometry : bond 0.00347 ( 4644) covalent geometry : angle 0.59951 ( 6292) *********************** 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: 11 poor density : 97 time to evaluate : 0.518 Fit side-chains REVERT: H 106 SER cc_start: 0.8780 (t) cc_final: 0.8575 (p) REVERT: H 116 GLU cc_start: 0.7785 (mp0) cc_final: 0.7391 (mp0) REVERT: H 130 SER cc_start: 0.8831 (t) cc_final: 0.8358 (m) REVERT: H 171 ASP cc_start: 0.8340 (p0) cc_final: 0.8032 (p0) REVERT: H 192 ASP cc_start: 0.8202 (m-30) cc_final: 0.7815 (m-30) REVERT: H 207 ASP cc_start: 0.8256 (t0) cc_final: 0.7838 (t0) REVERT: H 212 MET cc_start: 0.8983 (mmm) cc_final: 0.8728 (mmp) REVERT: H 249 ASP cc_start: 0.8456 (m-30) cc_final: 0.7875 (m-30) REVERT: H 251 GLU cc_start: 0.8773 (tt0) cc_final: 0.8126 (tp30) REVERT: H 252 ARG cc_start: 0.9077 (mtm-85) cc_final: 0.8659 (mtm-85) REVERT: H 284 ARG cc_start: 0.6120 (ttt180) cc_final: 0.4842 (mtp180) REVERT: H 301 ASP cc_start: 0.8179 (p0) cc_final: 0.7742 (p0) REVERT: H 319 THR cc_start: 0.9062 (p) cc_final: 0.8658 (p) REVERT: H 331 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: H 385 ASP cc_start: 0.8951 (t0) cc_final: 0.8716 (t0) REVERT: H 411 ASP cc_start: 0.8129 (t0) cc_final: 0.7846 (t0) REVERT: H 415 SER cc_start: 0.8909 (t) cc_final: 0.8423 (p) REVERT: H 428 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8158 (mt-10) REVERT: H 483 ARG cc_start: 0.8229 (ttt-90) cc_final: 0.7968 (ttt180) REVERT: H 489 CYS cc_start: 0.8508 (m) cc_final: 0.8251 (p) REVERT: H 525 MET cc_start: 0.8517 (mmt) cc_final: 0.8313 (mmm) REVERT: H 543 ILE cc_start: 0.9314 (mt) cc_final: 0.9028 (mm) REVERT: H 584 ASN cc_start: 0.8891 (t0) cc_final: 0.8292 (t160) REVERT: H 585 ASP cc_start: 0.7827 (t0) cc_final: 0.7536 (t0) REVERT: H 586 ASP cc_start: 0.7512 (m-30) cc_final: 0.7174 (m-30) outliers start: 11 outliers final: 5 residues processed: 106 average time/residue: 1.0165 time to fit residues: 112.7545 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 : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 243 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 576 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 0.0040 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.090131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080699 restraints weight = 8574.897| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.39 r_work: 0.3124 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4662 Z= 0.154 Angle : 0.619 7.576 6332 Z= 0.317 Chirality : 0.045 0.160 701 Planarity : 0.004 0.042 805 Dihedral : 6.340 51.710 796 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.86 % Allowed : 18.18 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.35), residues: 538 helix: 0.77 (0.59), residues: 83 sheet: 0.29 (0.42), residues: 150 loop : -0.44 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.031 0.002 PHE H 527 TYR 0.009 0.001 TYR H 81 ARG 0.005 0.000 ARG H 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 4) link_NAG-ASN : angle 1.30949 ( 12) link_BETA1-4 : bond 0.00387 ( 5) link_BETA1-4 : angle 1.26951 ( 15) hydrogen bonds : bond 0.03519 ( 150) hydrogen bonds : angle 5.37902 ( 375) link_BETA1-6 : bond 0.01538 ( 1) link_BETA1-6 : angle 2.04832 ( 3) metal coordination : bond 0.00896 ( 3) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.90957 ( 10) covalent geometry : bond 0.00352 ( 4644) covalent geometry : angle 0.61289 ( 6292) *********************** 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 105 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.064 Fit side-chains REVERT: H 106 SER cc_start: 0.8786 (t) cc_final: 0.8525 (p) REVERT: H 116 GLU cc_start: 0.7786 (mp0) cc_final: 0.7409 (mp0) REVERT: H 130 SER cc_start: 0.8827 (t) cc_final: 0.8356 (m) REVERT: H 166 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8375 (mm-30) REVERT: H 171 ASP cc_start: 0.8306 (p0) cc_final: 0.7998 (p0) REVERT: H 192 ASP cc_start: 0.8234 (m-30) cc_final: 0.7802 (m-30) REVERT: H 207 ASP cc_start: 0.8248 (t0) cc_final: 0.7749 (t0) REVERT: H 212 MET cc_start: 0.8973 (mmm) cc_final: 0.8606 (mmp) REVERT: H 249 ASP cc_start: 0.8429 (m-30) cc_final: 0.7876 (m-30) REVERT: H 251 GLU cc_start: 0.8786 (tt0) cc_final: 0.8132 (tp30) REVERT: H 252 ARG cc_start: 0.9072 (mtm-85) cc_final: 0.8617 (mtm-85) REVERT: H 284 ARG cc_start: 0.6117 (ttt180) cc_final: 0.4825 (mtp180) REVERT: H 301 ASP cc_start: 0.8255 (p0) cc_final: 0.7871 (p0) REVERT: H 319 THR cc_start: 0.9055 (p) cc_final: 0.8640 (m) REVERT: H 331 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: H 385 ASP cc_start: 0.8972 (t0) cc_final: 0.8741 (t0) REVERT: H 415 SER cc_start: 0.8902 (t) cc_final: 0.8439 (p) REVERT: H 428 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8140 (mt-10) REVERT: H 483 ARG cc_start: 0.8225 (ttt-90) cc_final: 0.7901 (ttt180) REVERT: H 489 CYS cc_start: 0.8506 (m) cc_final: 0.8274 (p) REVERT: H 543 ILE cc_start: 0.9305 (mt) cc_final: 0.9002 (mm) REVERT: H 584 ASN cc_start: 0.8906 (t0) cc_final: 0.8298 (t160) REVERT: H 585 ASP cc_start: 0.7914 (t0) cc_final: 0.7621 (t0) REVERT: H 586 ASP cc_start: 0.7598 (m-30) cc_final: 0.7203 (m-30) outliers start: 9 outliers final: 5 residues processed: 104 average time/residue: 1.1685 time to fit residues: 126.5578 Evaluate side-chains 96 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 244 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 576 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.089833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.080245 restraints weight = 8659.570| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.41 r_work: 0.3113 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4662 Z= 0.158 Angle : 0.628 8.213 6332 Z= 0.323 Chirality : 0.045 0.143 701 Planarity : 0.004 0.043 805 Dihedral : 5.538 51.198 796 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.45 % Allowed : 20.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.35), residues: 538 helix: 0.84 (0.59), residues: 83 sheet: 0.28 (0.42), residues: 150 loop : -0.43 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.033 0.002 PHE H 527 TYR 0.009 0.001 TYR H 81 ARG 0.005 0.000 ARG H 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 4) link_NAG-ASN : angle 1.44815 ( 12) link_BETA1-4 : bond 0.00405 ( 5) link_BETA1-4 : angle 1.33058 ( 15) hydrogen bonds : bond 0.03451 ( 150) hydrogen bonds : angle 5.39027 ( 375) link_BETA1-6 : bond 0.01319 ( 1) link_BETA1-6 : angle 1.47499 ( 3) metal coordination : bond 0.00907 ( 3) SS BOND : bond 0.00196 ( 5) SS BOND : angle 0.90313 ( 10) covalent geometry : bond 0.00362 ( 4644) covalent geometry : angle 0.62175 ( 6292) *********************** 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: 7 poor density : 95 time to evaluate : 0.573 Fit side-chains REVERT: H 106 SER cc_start: 0.8737 (t) cc_final: 0.8448 (p) REVERT: H 116 GLU cc_start: 0.7849 (mp0) cc_final: 0.7470 (mp0) REVERT: H 130 SER cc_start: 0.8816 (t) cc_final: 0.8341 (m) REVERT: H 171 ASP cc_start: 0.8301 (p0) cc_final: 0.7987 (p0) REVERT: H 192 ASP cc_start: 0.8236 (m-30) cc_final: 0.7769 (m-30) REVERT: H 207 ASP cc_start: 0.8261 (t0) cc_final: 0.7782 (t0) REVERT: H 212 MET cc_start: 0.8982 (mmm) cc_final: 0.8461 (mmm) REVERT: H 238 ILE cc_start: 0.9071 (mp) cc_final: 0.8806 (mp) REVERT: H 249 ASP cc_start: 0.8417 (m-30) cc_final: 0.7879 (m-30) REVERT: H 252 ARG cc_start: 0.9071 (mtm-85) cc_final: 0.8673 (mtm-85) REVERT: H 284 ARG cc_start: 0.6141 (ttt180) cc_final: 0.4865 (mtp180) REVERT: H 301 ASP cc_start: 0.8317 (p0) cc_final: 0.7947 (p0) REVERT: H 385 ASP cc_start: 0.8973 (t0) cc_final: 0.8744 (t0) REVERT: H 411 ASP cc_start: 0.8125 (t0) cc_final: 0.7882 (t70) REVERT: H 415 SER cc_start: 0.8840 (t) cc_final: 0.8486 (p) REVERT: H 428 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8165 (mt-10) REVERT: H 483 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.7854 (ttt180) REVERT: H 489 CYS cc_start: 0.8545 (m) cc_final: 0.8280 (p) REVERT: H 525 MET cc_start: 0.8549 (mmm) cc_final: 0.8147 (mmm) REVERT: H 543 ILE cc_start: 0.9286 (mt) cc_final: 0.8966 (mm) REVERT: H 574 GLN cc_start: 0.8380 (tt0) cc_final: 0.8154 (tt0) REVERT: H 578 ARG cc_start: 0.8784 (ptp90) cc_final: 0.8461 (ptp90) REVERT: H 584 ASN cc_start: 0.8919 (t0) cc_final: 0.8291 (t160) REVERT: H 585 ASP cc_start: 0.7933 (t0) cc_final: 0.7667 (t0) REVERT: H 586 ASP cc_start: 0.7595 (m-30) cc_final: 0.7220 (m-30) outliers start: 7 outliers final: 6 residues processed: 101 average time/residue: 1.5116 time to fit residues: 158.2189 Evaluate side-chains 97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 576 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.0170 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7618 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.089914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.080287 restraints weight = 8582.258| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.40 r_work: 0.3120 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4662 Z= 0.144 Angle : 0.649 12.865 6332 Z= 0.331 Chirality : 0.044 0.154 701 Planarity : 0.004 0.047 805 Dihedral : 5.157 51.525 796 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.24 % Allowed : 22.11 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.35), residues: 538 helix: 0.98 (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 TRP 0.024 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.035 0.002 PHE H 527 TYR 0.008 0.001 TYR H 81 ARG 0.008 0.001 ARG H 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 4) link_NAG-ASN : angle 1.32002 ( 12) link_BETA1-4 : bond 0.00391 ( 5) link_BETA1-4 : angle 1.29081 ( 15) hydrogen bonds : bond 0.03327 ( 150) hydrogen bonds : angle 5.38091 ( 375) link_BETA1-6 : bond 0.00893 ( 1) link_BETA1-6 : angle 1.18767 ( 3) metal coordination : bond 0.00751 ( 3) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.88269 ( 10) covalent geometry : bond 0.00334 ( 4644) covalent geometry : angle 0.64437 ( 6292) *********************** 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 104 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.657 Fit side-chains REVERT: H 106 SER cc_start: 0.8685 (t) cc_final: 0.8367 (p) REVERT: H 116 GLU cc_start: 0.7873 (mp0) cc_final: 0.7487 (mp0) REVERT: H 130 SER cc_start: 0.8813 (t) cc_final: 0.8341 (m) REVERT: H 171 ASP cc_start: 0.8292 (p0) cc_final: 0.7979 (p0) REVERT: H 192 ASP cc_start: 0.8194 (m-30) cc_final: 0.7746 (m-30) REVERT: H 207 ASP cc_start: 0.8239 (t0) cc_final: 0.7766 (t0) REVERT: H 212 MET cc_start: 0.8968 (mmm) cc_final: 0.8507 (mmm) REVERT: H 238 ILE cc_start: 0.9074 (mp) cc_final: 0.8794 (mp) REVERT: H 249 ASP cc_start: 0.8408 (m-30) cc_final: 0.7880 (m-30) REVERT: H 251 GLU cc_start: 0.8794 (tt0) cc_final: 0.8144 (tp30) REVERT: H 252 ARG cc_start: 0.9036 (mtm-85) cc_final: 0.8609 (mtm-85) REVERT: H 284 ARG cc_start: 0.6115 (ttt180) cc_final: 0.0916 (tmt170) REVERT: H 301 ASP cc_start: 0.8330 (p0) cc_final: 0.7946 (p0) REVERT: H 331 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: H 385 ASP cc_start: 0.8954 (t0) cc_final: 0.8719 (t0) REVERT: H 411 ASP cc_start: 0.8186 (t0) cc_final: 0.7906 (t70) REVERT: H 415 SER cc_start: 0.8846 (t) cc_final: 0.8456 (p) REVERT: H 428 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8094 (mt-10) REVERT: H 489 CYS cc_start: 0.8507 (m) cc_final: 0.8260 (p) REVERT: H 525 MET cc_start: 0.8520 (mmm) cc_final: 0.8148 (mmm) REVERT: H 543 ILE cc_start: 0.9258 (mt) cc_final: 0.8944 (mm) REVERT: H 574 GLN cc_start: 0.8358 (tt0) cc_final: 0.8121 (tt0) REVERT: H 578 ARG cc_start: 0.8754 (ptp90) cc_final: 0.8495 (ptp90) REVERT: H 584 ASN cc_start: 0.8911 (t0) cc_final: 0.8286 (t160) REVERT: H 585 ASP cc_start: 0.7944 (t0) cc_final: 0.7684 (t0) REVERT: H 586 ASP cc_start: 0.7612 (m-30) cc_final: 0.7235 (m-30) REVERT: H 594 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7504 (mp0) outliers start: 6 outliers final: 5 residues processed: 103 average time/residue: 1.1848 time to fit residues: 127.0984 Evaluate side-chains 97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 331 GLU Chi-restraints excluded: chain H residue 425 THR Chi-restraints excluded: chain H residue 552 THR Chi-restraints excluded: chain H residue 576 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN H 574 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.089140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079848 restraints weight = 8539.572| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.36 r_work: 0.3114 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 0.047 4662 Z= 0.160 Angle : 0.669 11.768 6332 Z= 0.340 Chirality : 0.045 0.148 701 Planarity : 0.004 0.049 805 Dihedral : 5.100 51.512 796 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.86 % Allowed : 21.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.35), residues: 538 helix: 0.93 (0.59), residues: 83 sheet: 0.41 (0.42), residues: 150 loop : -0.48 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.036 0.002 PHE H 527 TYR 0.009 0.001 TYR H 81 ARG 0.009 0.001 ARG H 483 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 4) link_NAG-ASN : angle 1.29204 ( 12) link_BETA1-4 : bond 0.00346 ( 5) link_BETA1-4 : angle 1.31119 ( 15) hydrogen bonds : bond 0.03471 ( 150) hydrogen bonds : angle 5.40306 ( 375) link_BETA1-6 : bond 0.00537 ( 1) link_BETA1-6 : angle 1.21573 ( 3) metal coordination : bond 0.00901 ( 3) SS BOND : bond 0.00193 ( 5) SS BOND : angle 0.92642 ( 10) covalent geometry : bond 0.00372 ( 4644) covalent geometry : angle 0.66371 ( 6292) *********************** 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 105 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: H 106 SER cc_start: 0.8684 (t) cc_final: 0.8350 (p) REVERT: H 116 GLU cc_start: 0.7870 (mp0) cc_final: 0.7553 (mp0) REVERT: H 130 SER cc_start: 0.8825 (t) cc_final: 0.8363 (m) REVERT: H 171 ASP cc_start: 0.8253 (p0) cc_final: 0.7947 (p0) REVERT: H 192 ASP cc_start: 0.8198 (m-30) cc_final: 0.7740 (m-30) REVERT: H 207 ASP cc_start: 0.8236 (t0) cc_final: 0.7769 (t0) REVERT: H 212 MET cc_start: 0.8999 (mmm) cc_final: 0.8520 (mmm) REVERT: H 249 ASP cc_start: 0.8386 (m-30) cc_final: 0.7886 (m-30) REVERT: H 252 ARG cc_start: 0.9030 (mtm-85) cc_final: 0.8812 (mtm-85) REVERT: H 284 ARG cc_start: 0.6150 (ttt180) cc_final: 0.4884 (mtp180) REVERT: H 301 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7972 (p0) REVERT: H 331 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: H 385 ASP cc_start: 0.8958 (t0) cc_final: 0.8745 (t0) REVERT: H 411 ASP cc_start: 0.8230 (t0) cc_final: 0.7945 (t70) REVERT: H 415 SER cc_start: 0.8835 (t) cc_final: 0.8418 (p) REVERT: H 428 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8143 (mt-10) REVERT: H 478 SER cc_start: 0.8123 (m) cc_final: 0.7534 (p) REVERT: H 489 CYS cc_start: 0.8515 (m) cc_final: 0.8253 (p) REVERT: H 525 MET cc_start: 0.8515 (mmm) cc_final: 0.8155 (mmm) REVERT: H 543 ILE cc_start: 0.9251 (mt) cc_final: 0.8937 (mm) REVERT: H 584 ASN cc_start: 0.8914 (t0) cc_final: 0.8295 (t160) REVERT: H 585 ASP cc_start: 0.7856 (t0) cc_final: 0.7616 (t0) REVERT: H 586 ASP cc_start: 0.7636 (m-30) cc_final: 0.7292 (m-30) REVERT: H 594 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7425 (mp0) outliers start: 9 outliers final: 8 residues processed: 103 average time/residue: 1.7534 time to fit residues: 189.5475 Evaluate side-chains 100 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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 329 LEU 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 Chi-restraints excluded: chain H residue 576 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 0.2980 chunk 23 optimal weight: 0.0470 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.090623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.081011 restraints weight = 8515.656| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.40 r_work: 0.3133 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4662 Z= 0.125 Angle : 0.665 11.919 6332 Z= 0.339 Chirality : 0.044 0.174 701 Planarity : 0.004 0.048 805 Dihedral : 4.985 51.838 796 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.35 % Favored : 96.47 % Rotamer: Outliers : 1.45 % Allowed : 21.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.36), residues: 538 helix: 1.08 (0.60), residues: 83 sheet: 0.48 (0.43), residues: 150 loop : -0.43 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.036 0.001 PHE H 527 TYR 0.008 0.001 TYR H 81 ARG 0.008 0.001 ARG H 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 4) link_NAG-ASN : angle 1.19963 ( 12) link_BETA1-4 : bond 0.00402 ( 5) link_BETA1-4 : angle 1.16573 ( 15) hydrogen bonds : bond 0.03232 ( 150) hydrogen bonds : angle 5.33753 ( 375) link_BETA1-6 : bond 0.00389 ( 1) link_BETA1-6 : angle 1.08845 ( 3) metal coordination : bond 0.00499 ( 3) SS BOND : bond 0.00157 ( 5) SS BOND : angle 0.85406 ( 10) covalent geometry : bond 0.00294 ( 4644) covalent geometry : angle 0.66098 ( 6292) ********************** 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 103 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 1.374 Fit side-chains REVERT: H 106 SER cc_start: 0.8548 (t) cc_final: 0.8214 (p) REVERT: H 116 GLU cc_start: 0.7836 (mp0) cc_final: 0.7539 (mp0) REVERT: H 130 SER cc_start: 0.8828 (t) cc_final: 0.8384 (m) REVERT: H 171 ASP cc_start: 0.8278 (p0) cc_final: 0.7936 (p0) REVERT: H 192 ASP cc_start: 0.8191 (m-30) cc_final: 0.7699 (m-30) REVERT: H 207 ASP cc_start: 0.8248 (t0) cc_final: 0.7774 (t0) REVERT: H 212 MET cc_start: 0.8949 (mmm) cc_final: 0.8412 (mmm) REVERT: H 249 ASP cc_start: 0.8388 (m-30) cc_final: 0.7884 (m-30) REVERT: H 252 ARG cc_start: 0.9021 (mtm-85) cc_final: 0.8800 (mtm-85) REVERT: H 284 ARG cc_start: 0.6071 (ttt180) cc_final: 0.0954 (tmt170) REVERT: H 301 ASP cc_start: 0.8333 (p0) cc_final: 0.7952 (p0) REVERT: H 331 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: H 385 ASP cc_start: 0.8961 (t0) cc_final: 0.8746 (t0) REVERT: H 411 ASP cc_start: 0.8205 (t0) cc_final: 0.7916 (t70) REVERT: H 415 SER cc_start: 0.8803 (t) cc_final: 0.8353 (p) REVERT: H 428 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8132 (mt-10) REVERT: H 446 GLU cc_start: 0.8319 (pp20) cc_final: 0.8020 (pp20) REVERT: H 478 SER cc_start: 0.8169 (m) cc_final: 0.7581 (p) REVERT: H 489 CYS cc_start: 0.8509 (m) cc_final: 0.8261 (p) REVERT: H 518 ARG cc_start: 0.9018 (mtm180) cc_final: 0.8756 (ttm110) REVERT: H 525 MET cc_start: 0.8520 (mmm) cc_final: 0.8142 (mmm) REVERT: H 543 ILE cc_start: 0.9210 (mt) cc_final: 0.8894 (mm) REVERT: H 584 ASN cc_start: 0.8898 (t0) cc_final: 0.8282 (t160) REVERT: H 585 ASP cc_start: 0.7921 (t0) cc_final: 0.7663 (t0) REVERT: H 586 ASP cc_start: 0.7596 (m-30) cc_final: 0.7164 (m-30) REVERT: H 594 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7444 (mp0) outliers start: 7 outliers final: 7 residues processed: 102 average time/residue: 1.4731 time to fit residues: 158.2394 Evaluate side-chains 100 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain H residue 576 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.089225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079632 restraints weight = 8545.654| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.42 r_work: 0.3105 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4527 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 : 0.663 11.613 6332 Z= 0.341 Chirality : 0.044 0.144 701 Planarity : 0.004 0.051 805 Dihedral : 5.042 51.808 796 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.53 % Favored : 96.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.36), residues: 538 helix: 1.05 (0.60), residues: 83 sheet: 0.49 (0.43), residues: 150 loop : -0.42 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.036 0.002 PHE H 527 TYR 0.009 0.001 TYR H 81 ARG 0.006 0.001 ARG H 483 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 4) link_NAG-ASN : angle 1.22061 ( 12) link_BETA1-4 : bond 0.00358 ( 5) link_BETA1-4 : angle 1.26087 ( 15) hydrogen bonds : bond 0.03307 ( 150) hydrogen bonds : angle 5.35807 ( 375) link_BETA1-6 : bond 0.00304 ( 1) link_BETA1-6 : angle 1.22529 ( 3) metal coordination : bond 0.00841 ( 3) SS BOND : bond 0.00173 ( 5) SS BOND : angle 0.89593 ( 10) covalent geometry : bond 0.00363 ( 4644) covalent geometry : angle 0.65848 ( 6292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4996.10 seconds wall clock time: 89 minutes 39.15 seconds (5379.15 seconds total)