Starting phenix.real_space_refine on Tue Feb 11 07:54:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uac_26420/02_2025/7uac_26420.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uac_26420/02_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_26420/02_2025/7uac_26420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uac_26420/02_2025/7uac_26420.map" model { file = "/net/cci-nas-00/data/ceres_data/7uac_26420/02_2025/7uac_26420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uac_26420/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.53, per 1000 atoms: 0.78 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: 1.36 Conformation dependent library (CDL) restraints added in 542.2 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: 0.60 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: 1.43 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 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: 0.820 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.280 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- 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 : 0.012 0.072 4644 Z= 0.766 Angle : 1.786 9.345 6292 Z= 1.201 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 *********************** 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 : 0.554 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: 1.3146 time to fit residues: 221.0468 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 : 0.533 ------------------------------------------------------------------------------- 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 = 27)----------------| | 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: 0.8408 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 4644 Z= 0.261 Angle : 0.713 8.559 6292 Z= 0.370 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 *********************** 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 : 0.483 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: 0.8819 (mttt) cc_final: 0.8612 (mttt) REVERT: H 116 GLU cc_start: 0.7371 (mp0) cc_final: 0.7016 (mp0) REVERT: H 117 SER cc_start: 0.8293 (m) cc_final: 0.8027 (p) REVERT: H 130 SER cc_start: 0.8821 (t) cc_final: 0.8331 (m) REVERT: H 192 ASP cc_start: 0.8213 (m-30) cc_final: 0.7871 (m-30) REVERT: H 207 ASP cc_start: 0.8303 (t0) cc_final: 0.7986 (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: 0.8182 (t0) REVERT: H 249 ASP cc_start: 0.8441 (m-30) cc_final: 0.8101 (m-30) REVERT: H 251 GLU cc_start: 0.8715 (tt0) cc_final: 0.8205 (tp30) REVERT: H 284 ARG cc_start: 0.5902 (ttt180) cc_final: 0.0618 (tmt170) REVERT: H 304 LEU cc_start: 0.9348 (mt) cc_final: 0.8950 (mm) REVERT: H 319 THR cc_start: 0.8863 (p) cc_final: 0.8567 (m) REVERT: H 329 LEU cc_start: 0.9140 (mt) cc_final: 0.8934 (mt) REVERT: H 331 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: H 385 ASP cc_start: 0.8814 (t0) cc_final: 0.8518 (t0) REVERT: H 415 SER cc_start: 0.8828 (t) cc_final: 0.8449 (p) REVERT: H 428 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8139 (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: 0.8498 (mmt) cc_final: 0.8246 (mmm) REVERT: H 543 ILE cc_start: 0.9382 (mt) cc_final: 0.9148 (mm) outliers start: 12 outliers final: 2 residues processed: 114 average time/residue: 1.2255 time to fit residues: 144.9486 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 : 0.493 ------------------------------------------------------------------------------- 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: 4.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.092465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082730 restraints weight = 8573.589| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.43 r_work: 0.3156 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4644 Z= 0.200 Angle : 0.637 7.139 6292 Z= 0.331 Chirality : 0.046 0.167 701 Planarity : 0.004 0.042 805 Dihedral : 10.017 108.617 796 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.07 % Allowed : 15.91 % Favored : 82.02 % 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: 0.10 (0.35), residues: 538 helix: 0.90 (0.61), residues: 77 sheet: 0.33 (0.42), residues: 144 loop : -0.20 (0.33), residues: 317 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 0.026 0.002 PHE H 527 TYR 0.009 0.001 TYR H 403 ARG 0.010 0.001 ARG H 546 *********************** 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 110 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.510 Fit side-chains REVERT: H 42 ASP cc_start: 0.7234 (p0) cc_final: 0.7011 (p0) REVERT: H 116 GLU cc_start: 0.7562 (mp0) cc_final: 0.7221 (mp0) REVERT: H 130 SER cc_start: 0.8825 (t) cc_final: 0.8344 (m) REVERT: H 192 ASP cc_start: 0.8249 (m-30) cc_final: 0.7874 (m-30) REVERT: H 207 ASP cc_start: 0.8306 (t0) cc_final: 0.7886 (t0) REVERT: H 212 MET cc_start: 0.8917 (mmm) cc_final: 0.8554 (mmp) REVERT: H 238 ILE cc_start: 0.9160 (mp) cc_final: 0.8942 (mp) REVERT: H 244 ASP cc_start: 0.8432 (t70) cc_final: 0.8112 (t0) REVERT: H 249 ASP cc_start: 0.8509 (m-30) cc_final: 0.7857 (m-30) REVERT: H 252 ARG cc_start: 0.9094 (mtm-85) cc_final: 0.8723 (mtm-85) REVERT: H 284 ARG cc_start: 0.5886 (ttt180) cc_final: 0.0756 (tmt170) REVERT: H 301 ASP cc_start: 0.7919 (p0) cc_final: 0.7496 (p0) REVERT: H 319 THR cc_start: 0.8966 (p) cc_final: 0.8359 (m) REVERT: H 331 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: H 385 ASP cc_start: 0.8909 (t0) cc_final: 0.8664 (t0) REVERT: H 411 ASP cc_start: 0.8131 (t0) cc_final: 0.7885 (t0) REVERT: H 415 SER cc_start: 0.8884 (t) cc_final: 0.8412 (p) REVERT: H 428 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8167 (mt-10) REVERT: H 483 ARG cc_start: 0.8169 (ttt-90) cc_final: 0.7904 (ttt180) REVERT: H 489 CYS cc_start: 0.8540 (m) cc_final: 0.8337 (m) REVERT: H 494 ASP cc_start: 0.8399 (p0) cc_final: 0.7529 (t0) REVERT: H 525 MET cc_start: 0.8518 (mmt) cc_final: 0.8294 (mmm) REVERT: H 543 ILE cc_start: 0.9356 (mt) cc_final: 0.9086 (mm) REVERT: H 546 ARG cc_start: 0.7885 (mtp-110) cc_final: 0.7152 (mmm160) REVERT: H 578 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8230 (ptp90) REVERT: H 586 ASP cc_start: 0.7584 (m-30) cc_final: 0.7309 (m-30) REVERT: H 594 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7646 (mm-30) outliers start: 10 outliers final: 4 residues processed: 108 average time/residue: 1.1308 time to fit residues: 126.9432 Evaluate side-chains 98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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: 1.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 0.0050 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.090921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.081262 restraints weight = 8677.588| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.44 r_work: 0.3135 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4644 Z= 0.197 Angle : 0.598 7.604 6292 Z= 0.312 Chirality : 0.044 0.164 701 Planarity : 0.004 0.043 805 Dihedral : 8.543 95.857 796 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.69 % Allowed : 16.53 % Favored : 80.79 % 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: 0.06 (0.35), residues: 538 helix: 0.93 (0.61), residues: 77 sheet: 0.36 (0.43), residues: 146 loop : -0.29 (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 0.001 PHE H 527 TYR 0.009 0.001 TYR H 403 ARG 0.006 0.001 ARG H 74 *********************** 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 111 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.499 Fit side-chains REVERT: H 116 GLU cc_start: 0.7687 (mp0) cc_final: 0.7308 (mp0) REVERT: H 130 SER cc_start: 0.8845 (t) cc_final: 0.8367 (m) REVERT: H 192 ASP cc_start: 0.8249 (m-30) cc_final: 0.7878 (m-30) REVERT: H 207 ASP cc_start: 0.8284 (t0) cc_final: 0.7890 (t0) REVERT: H 212 MET cc_start: 0.8939 (mmm) cc_final: 0.8548 (mmp) REVERT: H 249 ASP cc_start: 0.8457 (m-30) cc_final: 0.7835 (m-30) REVERT: H 251 GLU cc_start: 0.8754 (tt0) cc_final: 0.8103 (tp30) REVERT: H 252 ARG cc_start: 0.9072 (mtm-85) cc_final: 0.8690 (mtm-85) REVERT: H 284 ARG cc_start: 0.6043 (ttt180) cc_final: 0.4770 (mtp180) REVERT: H 301 ASP cc_start: 0.8017 (p0) cc_final: 0.7589 (p0) REVERT: H 319 THR cc_start: 0.9008 (p) cc_final: 0.8515 (m) REVERT: H 331 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: H 385 ASP cc_start: 0.8949 (t0) cc_final: 0.8694 (t0) REVERT: H 411 ASP cc_start: 0.8143 (t0) cc_final: 0.7796 (t0) REVERT: H 415 SER cc_start: 0.8899 (t) cc_final: 0.8421 (p) REVERT: H 423 ASP cc_start: 0.8584 (m-30) cc_final: 0.8221 (m-30) REVERT: H 425 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8373 (p) REVERT: H 428 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8196 (mt-10) REVERT: H 483 ARG cc_start: 0.8184 (ttt-90) cc_final: 0.7878 (ttt180) REVERT: H 489 CYS cc_start: 0.8555 (m) cc_final: 0.8237 (p) REVERT: H 494 ASP cc_start: 0.8488 (p0) cc_final: 0.8157 (p0) REVERT: H 525 MET cc_start: 0.8492 (mmt) cc_final: 0.8221 (mmm) REVERT: H 543 ILE cc_start: 0.9334 (mt) cc_final: 0.9067 (mm) REVERT: H 578 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8171 (ptp90) REVERT: H 584 ASN cc_start: 0.8818 (t0) cc_final: 0.8217 (t160) REVERT: H 585 ASP cc_start: 0.7786 (t0) cc_final: 0.7584 (t0) REVERT: H 586 ASP cc_start: 0.7500 (m-30) cc_final: 0.7134 (m-30) REVERT: H 594 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7687 (mm-30) outliers start: 13 outliers final: 3 residues processed: 109 average time/residue: 1.0764 time to fit residues: 122.1442 Evaluate side-chains 95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.090005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.080488 restraints weight = 8709.956| |-----------------------------------------------------------------------------| 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: 0.2977 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4644 Z= 0.226 Angle : 0.592 8.151 6292 Z= 0.306 Chirality : 0.044 0.162 701 Planarity : 0.004 0.043 805 Dihedral : 7.474 78.652 796 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.48 % Allowed : 17.15 % 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: -0.07 (0.35), residues: 538 helix: 0.69 (0.58), residues: 84 sheet: 0.51 (0.43), residues: 144 loop : -0.49 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.032 0.002 PHE H 37 TYR 0.009 0.001 TYR H 81 ARG 0.006 0.001 ARG H 546 *********************** 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 105 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.489 Fit side-chains REVERT: H 106 SER cc_start: 0.8762 (t) cc_final: 0.8553 (p) REVERT: H 116 GLU cc_start: 0.7791 (mp0) cc_final: 0.7389 (mp0) REVERT: H 130 SER cc_start: 0.8835 (t) cc_final: 0.8361 (m) REVERT: H 171 ASP cc_start: 0.8353 (p0) cc_final: 0.8037 (p0) REVERT: H 192 ASP cc_start: 0.8189 (m-30) cc_final: 0.7810 (m-30) REVERT: H 207 ASP cc_start: 0.8283 (t0) cc_final: 0.7859 (t0) REVERT: H 212 MET cc_start: 0.8977 (mmm) cc_final: 0.8712 (mmp) REVERT: H 249 ASP cc_start: 0.8448 (m-30) cc_final: 0.7865 (m-30) REVERT: H 251 GLU cc_start: 0.8763 (tt0) cc_final: 0.8124 (tp30) REVERT: H 252 ARG cc_start: 0.9079 (mtm-85) cc_final: 0.8657 (mtm-85) REVERT: H 284 ARG cc_start: 0.6120 (ttt180) cc_final: 0.4848 (mtp180) REVERT: H 301 ASP cc_start: 0.8171 (p0) cc_final: 0.7735 (p0) REVERT: H 325 GLU cc_start: 0.8479 (pm20) cc_final: 0.8269 (pm20) REVERT: H 331 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: H 385 ASP cc_start: 0.8955 (t0) cc_final: 0.8719 (t0) REVERT: H 411 ASP cc_start: 0.8115 (t0) cc_final: 0.7834 (t0) REVERT: H 415 SER cc_start: 0.8898 (t) cc_final: 0.8504 (p) REVERT: H 428 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8132 (mt-10) REVERT: H 483 ARG cc_start: 0.8221 (ttt-90) cc_final: 0.7903 (ttt180) REVERT: H 489 CYS cc_start: 0.8498 (m) cc_final: 0.8241 (p) REVERT: H 525 MET cc_start: 0.8508 (mmt) cc_final: 0.8301 (mmm) REVERT: H 543 ILE cc_start: 0.9308 (mt) cc_final: 0.9020 (mm) REVERT: H 584 ASN cc_start: 0.8879 (t0) cc_final: 0.8275 (t160) REVERT: H 585 ASP cc_start: 0.7832 (t0) cc_final: 0.7540 (t0) REVERT: H 586 ASP cc_start: 0.7525 (m-30) cc_final: 0.7189 (m-30) REVERT: H 594 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7598 (mm-30) outliers start: 12 outliers final: 5 residues processed: 104 average time/residue: 0.9614 time to fit residues: 104.4967 Evaluate side-chains 90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 576 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.090023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.080547 restraints weight = 8598.303| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.40 r_work: 0.3138 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4644 Z= 0.231 Angle : 0.592 7.516 6292 Z= 0.307 Chirality : 0.045 0.160 701 Planarity : 0.004 0.042 805 Dihedral : 6.260 51.651 796 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.86 % Allowed : 17.98 % Favored : 80.17 % 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: 0.76 (0.59), residues: 83 sheet: 0.29 (0.42), residues: 150 loop : -0.42 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.029 0.002 PHE H 527 TYR 0.009 0.001 TYR H 81 ARG 0.005 0.000 ARG H 546 *********************** 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 108 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.550 Fit side-chains REVERT: H 106 SER cc_start: 0.8803 (t) cc_final: 0.8556 (p) REVERT: H 116 GLU cc_start: 0.7801 (mp0) cc_final: 0.7437 (mp0) REVERT: H 130 SER cc_start: 0.8813 (t) cc_final: 0.8365 (m) REVERT: H 166 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8305 (mm-30) REVERT: H 171 ASP cc_start: 0.8278 (p0) cc_final: 0.7974 (p0) REVERT: H 192 ASP cc_start: 0.8132 (m-30) cc_final: 0.7764 (m-30) REVERT: H 207 ASP cc_start: 0.8238 (t0) cc_final: 0.7765 (t0) REVERT: H 212 MET cc_start: 0.8981 (mmm) cc_final: 0.8653 (mmp) REVERT: H 249 ASP cc_start: 0.8410 (m-30) cc_final: 0.7889 (m-30) REVERT: H 251 GLU cc_start: 0.8772 (tt0) cc_final: 0.8157 (tp30) REVERT: H 252 ARG cc_start: 0.9083 (mtm-85) cc_final: 0.8633 (mtm-85) REVERT: H 284 ARG cc_start: 0.6082 (ttt180) cc_final: 0.4822 (mtp180) REVERT: H 301 ASP cc_start: 0.8281 (p0) cc_final: 0.7907 (p0) REVERT: H 319 THR cc_start: 0.9033 (p) cc_final: 0.8624 (m) REVERT: H 331 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: H 385 ASP cc_start: 0.8953 (t0) cc_final: 0.8737 (t0) REVERT: H 415 SER cc_start: 0.8902 (t) cc_final: 0.8461 (p) REVERT: H 428 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8102 (mt-10) REVERT: H 483 ARG cc_start: 0.8216 (ttt-90) cc_final: 0.7897 (ttt180) REVERT: H 489 CYS cc_start: 0.8516 (m) cc_final: 0.8313 (p) REVERT: H 543 ILE cc_start: 0.9300 (mt) cc_final: 0.9013 (mm) REVERT: H 584 ASN cc_start: 0.8893 (t0) cc_final: 0.8305 (t160) REVERT: H 585 ASP cc_start: 0.7914 (t0) cc_final: 0.7617 (t0) REVERT: H 586 ASP cc_start: 0.7602 (m-30) cc_final: 0.7235 (m-30) REVERT: H 594 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7584 (mm-30) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 1.0536 time to fit residues: 117.4711 Evaluate side-chains 95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 4.9990 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.089861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.080313 restraints weight = 8663.570| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.41 r_work: 0.3116 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4644 Z= 0.231 Angle : 0.618 8.192 6292 Z= 0.317 Chirality : 0.045 0.155 701 Planarity : 0.004 0.043 805 Dihedral : 5.498 51.086 796 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % 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: -0.01 (0.35), residues: 538 helix: 0.83 (0.59), residues: 83 sheet: 0.31 (0.42), residues: 150 loop : -0.35 (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 0.032 0.002 PHE H 527 TYR 0.009 0.001 TYR H 81 ARG 0.005 0.001 ARG H 546 *********************** 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 98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.594 Fit side-chains REVERT: H 106 SER cc_start: 0.8741 (t) cc_final: 0.8451 (p) REVERT: H 116 GLU cc_start: 0.7858 (mp0) cc_final: 0.7474 (mp0) REVERT: H 130 SER cc_start: 0.8813 (t) cc_final: 0.8348 (m) REVERT: H 171 ASP cc_start: 0.8267 (p0) cc_final: 0.7952 (p0) REVERT: H 192 ASP cc_start: 0.8164 (m-30) cc_final: 0.7774 (m-30) REVERT: H 207 ASP cc_start: 0.8275 (t0) cc_final: 0.7796 (t0) REVERT: H 212 MET cc_start: 0.8983 (mmm) cc_final: 0.8523 (mmm) REVERT: H 238 ILE cc_start: 0.9091 (mp) cc_final: 0.8813 (mp) REVERT: H 249 ASP cc_start: 0.8431 (m-30) cc_final: 0.7881 (m-30) REVERT: H 251 GLU cc_start: 0.8780 (tt0) cc_final: 0.8128 (tp30) REVERT: H 252 ARG cc_start: 0.9040 (mtm-85) cc_final: 0.8630 (mtm-85) REVERT: H 284 ARG cc_start: 0.6150 (ttt180) cc_final: 0.4879 (mtp180) REVERT: H 301 ASP cc_start: 0.8326 (p0) cc_final: 0.7968 (p0) REVERT: H 331 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: H 385 ASP cc_start: 0.8964 (t0) cc_final: 0.8740 (t0) REVERT: H 411 ASP cc_start: 0.8028 (t0) cc_final: 0.7756 (t70) REVERT: H 415 SER cc_start: 0.8812 (t) cc_final: 0.8477 (p) REVERT: H 428 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8127 (mt-10) REVERT: H 483 ARG cc_start: 0.8209 (ttt-90) cc_final: 0.7869 (ttt180) REVERT: H 489 CYS cc_start: 0.8529 (m) cc_final: 0.8270 (p) REVERT: H 525 MET cc_start: 0.8558 (mmm) cc_final: 0.8176 (mmm) REVERT: H 543 ILE cc_start: 0.9294 (mt) cc_final: 0.8985 (mm) REVERT: H 574 GLN cc_start: 0.8362 (tt0) cc_final: 0.8130 (tt0) REVERT: H 578 ARG cc_start: 0.8793 (ptp90) cc_final: 0.8524 (ptp90) REVERT: H 584 ASN cc_start: 0.8926 (t0) cc_final: 0.8307 (t160) REVERT: H 585 ASP cc_start: 0.7948 (t0) cc_final: 0.7683 (t0) REVERT: H 586 ASP cc_start: 0.7613 (m-30) cc_final: 0.7240 (m-30) REVERT: H 594 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7613 (mm-30) outliers start: 8 outliers final: 6 residues processed: 97 average time/residue: 1.1042 time to fit residues: 111.6384 Evaluate side-chains 92 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 576 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 574 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080376 restraints weight = 8612.046| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.39 r_work: 0.3119 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4644 Z= 0.226 Angle : 0.632 12.681 6292 Z= 0.322 Chirality : 0.044 0.155 701 Planarity : 0.004 0.046 805 Dihedral : 5.203 51.407 796 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.65 % Allowed : 20.87 % 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 (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: 0.90 (0.59), residues: 83 sheet: 0.37 (0.42), residues: 150 loop : -0.38 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.035 0.002 PHE H 527 TYR 0.009 0.001 TYR H 81 ARG 0.006 0.000 ARG H 546 *********************** 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: 8 poor density : 91 time to evaluate : 0.505 Fit side-chains REVERT: H 106 SER cc_start: 0.8709 (t) cc_final: 0.8397 (p) REVERT: H 116 GLU cc_start: 0.7863 (mp0) cc_final: 0.7474 (mp0) REVERT: H 130 SER cc_start: 0.8821 (t) cc_final: 0.8354 (m) REVERT: H 171 ASP cc_start: 0.8297 (p0) cc_final: 0.7985 (p0) REVERT: H 192 ASP cc_start: 0.8223 (m-30) cc_final: 0.7711 (m-30) REVERT: H 207 ASP cc_start: 0.8255 (t0) cc_final: 0.7779 (t0) REVERT: H 212 MET cc_start: 0.8984 (mmm) cc_final: 0.8523 (mmm) REVERT: H 238 ILE cc_start: 0.9087 (mp) cc_final: 0.8778 (mp) REVERT: H 249 ASP cc_start: 0.8395 (m-30) cc_final: 0.7879 (m-30) REVERT: H 251 GLU cc_start: 0.8778 (tt0) cc_final: 0.8131 (tp30) REVERT: H 252 ARG cc_start: 0.9038 (mtm-85) cc_final: 0.8643 (mtm-85) REVERT: H 284 ARG cc_start: 0.6142 (ttt180) cc_final: 0.4867 (mtp180) REVERT: H 301 ASP cc_start: 0.8339 (p0) cc_final: 0.7976 (p0) REVERT: H 331 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: H 385 ASP cc_start: 0.8977 (t0) cc_final: 0.8753 (t0) REVERT: H 411 ASP cc_start: 0.8084 (t0) cc_final: 0.7780 (t70) REVERT: H 415 SER cc_start: 0.8806 (t) cc_final: 0.8447 (p) REVERT: H 428 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8184 (mt-10) REVERT: H 483 ARG cc_start: 0.8200 (ttt-90) cc_final: 0.7855 (ttt180) REVERT: H 489 CYS cc_start: 0.8479 (m) cc_final: 0.8247 (p) REVERT: H 525 MET cc_start: 0.8544 (mmm) cc_final: 0.8146 (mmm) REVERT: H 543 ILE cc_start: 0.9266 (mt) cc_final: 0.8953 (mm) REVERT: H 578 ARG cc_start: 0.8758 (ptp90) cc_final: 0.8491 (ptp90) REVERT: H 584 ASN cc_start: 0.8925 (t0) cc_final: 0.8303 (t160) REVERT: H 585 ASP cc_start: 0.7972 (t0) cc_final: 0.7711 (t0) REVERT: H 586 ASP cc_start: 0.7625 (m-30) cc_final: 0.7251 (m-30) REVERT: H 594 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7633 (mm-30) outliers start: 8 outliers final: 6 residues processed: 98 average time/residue: 1.0686 time to fit residues: 109.2458 Evaluate side-chains 95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.089557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.080107 restraints weight = 8582.596| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.40 r_work: 0.3117 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4644 Z= 0.230 Angle : 0.630 11.769 6292 Z= 0.320 Chirality : 0.044 0.148 701 Planarity : 0.004 0.048 805 Dihedral : 5.130 51.459 796 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.16 % Favored : 96.65 % 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: 0.02 (0.36), residues: 538 helix: 0.90 (0.59), residues: 83 sheet: 0.40 (0.43), residues: 150 loop : -0.38 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.035 0.002 PHE H 527 TYR 0.009 0.001 TYR H 81 ARG 0.005 0.000 ARG H 546 *********************** 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 106 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: H 106 SER cc_start: 0.8699 (t) cc_final: 0.8368 (p) REVERT: H 116 GLU cc_start: 0.7850 (mp0) cc_final: 0.7539 (mp0) REVERT: H 130 SER cc_start: 0.8810 (t) cc_final: 0.8349 (m) REVERT: H 171 ASP cc_start: 0.8295 (p0) cc_final: 0.7984 (p0) REVERT: H 192 ASP cc_start: 0.8206 (m-30) cc_final: 0.7691 (m-30) REVERT: H 207 ASP cc_start: 0.8269 (t0) cc_final: 0.7786 (t0) REVERT: H 212 MET cc_start: 0.8985 (mmm) cc_final: 0.8514 (mmm) REVERT: H 249 ASP cc_start: 0.8405 (m-30) cc_final: 0.7882 (m-30) REVERT: H 251 GLU cc_start: 0.8794 (tt0) cc_final: 0.8137 (tp30) REVERT: H 252 ARG cc_start: 0.9040 (mtm-85) cc_final: 0.8599 (mtm-85) REVERT: H 284 ARG cc_start: 0.6186 (ttt180) cc_final: 0.4918 (mtp180) REVERT: H 301 ASP cc_start: 0.8369 (p0) cc_final: 0.8002 (p0) REVERT: H 319 THR cc_start: 0.9068 (p) cc_final: 0.8736 (m) REVERT: H 385 ASP cc_start: 0.8997 (t0) cc_final: 0.8762 (t0) REVERT: H 411 ASP cc_start: 0.8203 (t0) cc_final: 0.7908 (t70) REVERT: H 415 SER cc_start: 0.8807 (t) cc_final: 0.8351 (p) REVERT: H 428 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8171 (mt-10) REVERT: H 447 ASN cc_start: 0.8777 (m-40) cc_final: 0.8429 (m-40) REVERT: H 478 SER cc_start: 0.8083 (m) cc_final: 0.7501 (p) REVERT: H 489 CYS cc_start: 0.8503 (m) cc_final: 0.8248 (p) REVERT: H 525 MET cc_start: 0.8581 (mmm) cc_final: 0.8207 (mmm) REVERT: H 543 ILE cc_start: 0.9254 (mt) cc_final: 0.8948 (mm) REVERT: H 584 ASN cc_start: 0.8925 (t0) cc_final: 0.8311 (t160) REVERT: H 585 ASP cc_start: 0.7877 (t0) cc_final: 0.7630 (t0) REVERT: H 586 ASP cc_start: 0.7605 (m-30) cc_final: 0.7252 (m-30) REVERT: H 594 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7631 (mm-30) outliers start: 7 outliers final: 8 residues processed: 105 average time/residue: 1.1416 time to fit residues: 124.8030 Evaluate side-chains 102 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 190 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.079785 restraints weight = 8529.797| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.41 r_work: 0.3116 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4644 Z= 0.219 Angle : 0.653 11.747 6292 Z= 0.333 Chirality : 0.044 0.157 701 Planarity : 0.004 0.048 805 Dihedral : 5.065 51.549 796 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.16 % Favored : 96.65 % Rotamer: Outliers : 1.45 % Allowed : 21.69 % Favored : 76.86 % 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: 0.10 (0.36), residues: 538 helix: 1.00 (0.60), residues: 83 sheet: 0.46 (0.43), residues: 150 loop : -0.35 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 567 HIS 0.005 0.001 HIS H 155 PHE 0.036 0.002 PHE H 527 TYR 0.008 0.001 TYR H 81 ARG 0.008 0.001 ARG H 74 ********************** 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 99 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.511 Fit side-chains REVERT: H 106 SER cc_start: 0.8676 (t) cc_final: 0.8340 (p) REVERT: H 116 GLU cc_start: 0.7851 (mp0) cc_final: 0.7547 (mp0) REVERT: H 130 SER cc_start: 0.8830 (t) cc_final: 0.8370 (m) REVERT: H 171 ASP cc_start: 0.8289 (p0) cc_final: 0.7954 (p0) REVERT: H 192 ASP cc_start: 0.8229 (m-30) cc_final: 0.7736 (m-30) REVERT: H 207 ASP cc_start: 0.8256 (t0) cc_final: 0.7780 (t0) REVERT: H 212 MET cc_start: 0.8970 (mmm) cc_final: 0.8494 (mmm) REVERT: H 249 ASP cc_start: 0.8389 (m-30) cc_final: 0.7878 (m-30) REVERT: H 251 GLU cc_start: 0.8768 (tt0) cc_final: 0.8106 (tp30) REVERT: H 252 ARG cc_start: 0.9027 (mtm-85) cc_final: 0.8621 (mtm-85) REVERT: H 284 ARG cc_start: 0.6077 (ttt180) cc_final: 0.1015 (tmt170) REVERT: H 301 ASP cc_start: 0.8367 (p0) cc_final: 0.7993 (p0) REVERT: H 331 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: H 385 ASP cc_start: 0.8976 (t0) cc_final: 0.8751 (t0) REVERT: H 411 ASP cc_start: 0.8195 (t0) cc_final: 0.7902 (t70) REVERT: H 415 SER cc_start: 0.8810 (t) cc_final: 0.8407 (p) REVERT: H 428 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8159 (mt-10) REVERT: H 446 GLU cc_start: 0.8285 (pp20) cc_final: 0.8061 (pp20) REVERT: H 478 SER cc_start: 0.8152 (m) cc_final: 0.7579 (p) REVERT: H 489 CYS cc_start: 0.8498 (m) cc_final: 0.8250 (p) REVERT: H 525 MET cc_start: 0.8525 (mmm) cc_final: 0.8144 (mmm) REVERT: H 530 SER cc_start: 0.8847 (t) cc_final: 0.8634 (p) REVERT: H 543 ILE cc_start: 0.9237 (mt) cc_final: 0.8928 (mm) REVERT: H 584 ASN cc_start: 0.8926 (t0) cc_final: 0.8315 (t160) REVERT: H 585 ASP cc_start: 0.7948 (t0) cc_final: 0.7694 (t0) REVERT: H 586 ASP cc_start: 0.7625 (m-30) cc_final: 0.7272 (m-30) REVERT: H 594 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7607 (mm-30) outliers start: 7 outliers final: 7 residues processed: 98 average time/residue: 1.0639 time to fit residues: 108.7516 Evaluate side-chains 95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.089151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.079953 restraints weight = 8579.555| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.37 r_work: 0.3114 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4644 Z= 0.232 Angle : 0.650 11.665 6292 Z= 0.334 Chirality : 0.044 0.150 701 Planarity : 0.004 0.051 805 Dihedral : 5.058 51.622 796 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.53 % Favored : 96.28 % Rotamer: Outliers : 1.65 % Allowed : 21.49 % Favored : 76.86 % 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 (0.36), residues: 538 helix: 0.99 (0.60), residues: 83 sheet: 0.50 (0.43), residues: 150 loop : -0.39 (0.35), 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 0.007 0.001 ARG H 483 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4186.14 seconds wall clock time: 74 minutes 21.78 seconds (4461.78 seconds total)