Starting phenix.real_space_refine on Fri Oct 10 14:52:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qhp_18415/10_2025/8qhp_18415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qhp_18415/10_2025/8qhp_18415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qhp_18415/10_2025/8qhp_18415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qhp_18415/10_2025/8qhp_18415.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qhp_18415/10_2025/8qhp_18415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qhp_18415/10_2025/8qhp_18415.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 22 5.16 5 C 4392 2.51 5 N 1128 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6788 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3393 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 393} Chain breaks: 1 Chain: "B" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3393 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 393} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 236 SG CYS A 28 36.433 38.017 33.062 1.00137.77 S ATOM 1644 SG CYS A 208 33.883 39.740 30.430 1.00155.64 S ATOM 3629 SG CYS B 28 36.336 40.874 90.477 1.00138.97 S ATOM 5037 SG CYS B 208 37.721 38.524 92.922 1.00158.95 S Time building chain proxies: 1.85, per 1000 atoms: 0.27 Number of scatterers: 6788 At special positions: 0 Unit cell: (67.518, 71.148, 124.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 22 16.00 O 1244 8.00 N 1128 7.00 C 4392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 379.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 208 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 233 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 28 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 28 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 208 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 233 " 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1520 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 55.7% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 37 through 57 Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 86 through 103 Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.540A pdb=" N LEU A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.974A pdb=" N SER A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.679A pdb=" N PHE A 231 " --> pdb=" O ASP A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 304 through 329 Processing helix chain 'A' and resid 339 through 362 Processing helix chain 'A' and resid 365 through 387 Processing helix chain 'A' and resid 391 through 410 removed outlier: 3.502A pdb=" N LEU A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.715A pdb=" N GLU A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 57 Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 84 through 103 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.572A pdb=" N LEU B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.927A pdb=" N SER B 209 " --> pdb=" O HIS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 304 through 332 removed outlier: 3.710A pdb=" N ARG B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN B 331 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 362 Processing helix chain 'B' and resid 365 through 387 Processing helix chain 'B' and resid 391 through 410 Processing helix chain 'B' and resid 412 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 65 removed outlier: 9.433A pdb=" N PHE A 220 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS A 24 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP A 221 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU A 254 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS A 223 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR A 256 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY A 225 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 136 removed outlier: 6.453A pdb=" N ILE A 141 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 180 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 65 removed outlier: 11.532A pdb=" N GLU B 22 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE B 222 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS B 24 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY B 224 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR B 26 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLY B 226 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP B 221 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU B 254 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS B 223 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR B 256 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY B 225 " --> pdb=" O THR B 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 136 removed outlier: 6.385A pdb=" N ILE B 141 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 180 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 264 through 265 363 hydrogen bonds defined for protein. 1071 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: 1.09 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2164 1.34 - 1.46: 1623 1.46 - 1.58: 3137 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 6962 Sorted by residual: bond pdb=" N VAL B 32 " pdb=" CA VAL B 32 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.15e+00 bond pdb=" CA VAL A 32 " pdb=" C VAL A 32 " ideal model delta sigma weight residual 1.526 1.535 -0.008 9.00e-03 1.23e+04 8.57e-01 bond pdb=" CG ARG A 51 " pdb=" CD ARG A 51 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.18e-01 bond pdb=" CG1 ILE B 93 " pdb=" CD1 ILE B 93 " ideal model delta sigma weight residual 1.513 1.487 0.026 3.90e-02 6.57e+02 4.51e-01 bond pdb=" C ASP A 84 " pdb=" N PRO A 85 " ideal model delta sigma weight residual 1.336 1.342 -0.007 1.08e-02 8.57e+03 3.82e-01 ... (remaining 6957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 9020 0.85 - 1.70: 300 1.70 - 2.56: 23 2.56 - 3.41: 26 3.41 - 4.26: 1 Bond angle restraints: 9370 Sorted by residual: angle pdb=" N VAL B 32 " pdb=" CA VAL B 32 " pdb=" C VAL B 32 " ideal model delta sigma weight residual 106.21 110.47 -4.26 1.07e+00 8.73e-01 1.58e+01 angle pdb=" C VAL B 32 " pdb=" CA VAL B 32 " pdb=" CB VAL B 32 " ideal model delta sigma weight residual 113.22 110.73 2.49 1.12e+00 7.97e-01 4.93e+00 angle pdb=" CA VAL B 32 " pdb=" C VAL B 32 " pdb=" O VAL B 32 " ideal model delta sigma weight residual 122.63 120.99 1.64 8.70e-01 1.32e+00 3.56e+00 angle pdb=" CA TYR A 44 " pdb=" CB TYR A 44 " pdb=" CG TYR A 44 " ideal model delta sigma weight residual 113.90 111.19 2.71 1.80e+00 3.09e-01 2.27e+00 angle pdb=" CA TYR B 44 " pdb=" CB TYR B 44 " pdb=" CG TYR B 44 " ideal model delta sigma weight residual 113.90 111.31 2.59 1.80e+00 3.09e-01 2.07e+00 ... (remaining 9365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.35: 3658 12.35 - 24.70: 347 24.70 - 37.05: 86 37.05 - 49.40: 34 49.40 - 61.75: 19 Dihedral angle restraints: 4144 sinusoidal: 1762 harmonic: 2382 Sorted by residual: dihedral pdb=" CA LYS B 57 " pdb=" CB LYS B 57 " pdb=" CG LYS B 57 " pdb=" CD LYS B 57 " ideal model delta sinusoidal sigma weight residual -60.00 -119.56 59.56 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS A 295 " pdb=" CB LYS A 295 " pdb=" CG LYS A 295 " pdb=" CD LYS A 295 " ideal model delta sinusoidal sigma weight residual -60.00 -118.96 58.96 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG A 51 " pdb=" CB ARG A 51 " pdb=" CG ARG A 51 " pdb=" CD ARG A 51 " ideal model delta sinusoidal sigma weight residual -180.00 -123.05 -56.95 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 4141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 570 0.027 - 0.054: 237 0.054 - 0.082: 109 0.082 - 0.109: 33 0.109 - 0.136: 7 Chirality restraints: 956 Sorted by residual: chirality pdb=" CA ILE B 141 " pdb=" N ILE B 141 " pdb=" C ILE B 141 " pdb=" CB ILE B 141 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE A 141 " pdb=" N ILE A 141 " pdb=" C ILE A 141 " pdb=" CB ILE A 141 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA PHE A 92 " pdb=" N PHE A 92 " pdb=" C PHE A 92 " pdb=" CB PHE A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 953 not shown) Planarity restraints: 1202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 195 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.46e+00 pdb=" N PRO A 196 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 201 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 202 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 148 " 0.018 5.00e-02 4.00e+02 2.70e-02 1.16e+00 pdb=" N PRO B 149 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 149 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 149 " 0.015 5.00e-02 4.00e+02 ... (remaining 1199 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 235 2.72 - 3.27: 6703 3.27 - 3.81: 11579 3.81 - 4.36: 14304 4.36 - 4.90: 24475 Nonbonded interactions: 57296 Sorted by model distance: nonbonded pdb=" OE2 GLU B 237 " pdb="ZN ZN B 501 " model vdw 2.176 2.230 nonbonded pdb=" OG SER B 195 " pdb=" O GLY B 198 " model vdw 2.192 3.040 nonbonded pdb=" OE1 GLU B 286 " pdb=" OH TYR B 319 " model vdw 2.194 3.040 nonbonded pdb=" OG SER A 335 " pdb=" O ASP B 109 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP A 139 " pdb=" OH TYR A 142 " model vdw 2.219 3.040 ... (remaining 57291 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.090 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.990 Find NCS groups from input model: 0.110 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.002 0.026 6968 Z= 0.105 Angle : 0.384 4.260 9370 Z= 0.218 Chirality : 0.038 0.136 956 Planarity : 0.003 0.030 1202 Dihedral : 11.643 61.754 2624 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.29), residues: 812 helix: 1.87 (0.25), residues: 424 sheet: 0.25 (0.53), residues: 84 loop : 0.61 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.010 0.001 TYR A 44 PHE 0.007 0.001 PHE B 356 TRP 0.008 0.001 TRP A 249 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 6962) covalent geometry : angle 0.38369 ( 9370) hydrogen bonds : bond 0.12780 ( 363) hydrogen bonds : angle 5.33363 ( 1071) metal coordination : bond 0.00185 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.307 Fit side-chains REVERT: A 86 LYS cc_start: 0.8638 (tttt) cc_final: 0.8371 (tppt) REVERT: A 185 LYS cc_start: 0.9067 (mttt) cc_final: 0.8815 (mtmm) REVERT: A 199 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8222 (mt-10) REVERT: B 76 LYS cc_start: 0.8952 (tppp) cc_final: 0.8717 (ttmm) REVERT: B 90 GLU cc_start: 0.8410 (tt0) cc_final: 0.7956 (tm-30) REVERT: B 207 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7598 (pt0) REVERT: B 382 LYS cc_start: 0.8817 (tttt) cc_final: 0.8560 (tppp) REVERT: B 386 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8662 (mt-10) REVERT: B 414 ASP cc_start: 0.8827 (m-30) cc_final: 0.8347 (t0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.7439 time to fit residues: 84.4961 Evaluate side-chains 80 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 11 GLN B 66 ASN B 233 HIS B 309 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.077659 restraints weight = 9778.737| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.91 r_work: 0.2714 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 1.917 6968 Z= 0.777 Angle : 0.453 11.273 9370 Z= 0.235 Chirality : 0.039 0.160 956 Planarity : 0.003 0.035 1202 Dihedral : 3.761 14.547 902 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.82 % Allowed : 9.50 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.29), residues: 812 helix: 2.04 (0.25), residues: 442 sheet: 0.09 (0.49), residues: 92 loop : 0.91 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 77 TYR 0.012 0.001 TYR A 44 PHE 0.010 0.001 PHE A 92 TRP 0.007 0.001 TRP A 249 HIS 0.002 0.000 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6962) covalent geometry : angle 0.45290 ( 9370) hydrogen bonds : bond 0.03992 ( 363) hydrogen bonds : angle 4.25806 ( 1071) metal coordination : bond 0.78267 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.277 Fit side-chains REVERT: A 63 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8505 (tmm) REVERT: A 86 LYS cc_start: 0.8480 (tttt) cc_final: 0.8182 (tppt) REVERT: A 146 LYS cc_start: 0.8488 (mppt) cc_final: 0.8243 (mptt) REVERT: A 185 LYS cc_start: 0.8965 (mttt) cc_final: 0.8660 (mtmm) REVERT: A 199 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8068 (mt-10) REVERT: B 71 ASP cc_start: 0.8493 (t0) cc_final: 0.8143 (t0) REVERT: B 90 GLU cc_start: 0.8402 (tt0) cc_final: 0.7917 (tm-30) REVERT: B 382 LYS cc_start: 0.8747 (tttt) cc_final: 0.8473 (tppp) REVERT: B 386 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8746 (mt-10) outliers start: 13 outliers final: 4 residues processed: 102 average time/residue: 0.6797 time to fit residues: 72.3174 Evaluate side-chains 83 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 69 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 294 GLN B 11 GLN B 309 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.115346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.077287 restraints weight = 9473.317| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.90 r_work: 0.2698 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6968 Z= 0.138 Angle : 0.447 12.657 9370 Z= 0.232 Chirality : 0.039 0.144 956 Planarity : 0.003 0.035 1202 Dihedral : 3.703 14.350 902 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.54 % Allowed : 11.45 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.30), residues: 812 helix: 2.20 (0.25), residues: 442 sheet: -0.00 (0.49), residues: 92 loop : 1.04 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 77 TYR 0.012 0.001 TYR B 44 PHE 0.008 0.001 PHE B 47 TRP 0.006 0.001 TRP A 249 HIS 0.021 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6962) covalent geometry : angle 0.44655 ( 9370) hydrogen bonds : bond 0.03833 ( 363) hydrogen bonds : angle 4.07367 ( 1071) metal coordination : bond 0.03165 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8569 (ttm) REVERT: A 86 LYS cc_start: 0.8466 (tttt) cc_final: 0.8182 (tppt) REVERT: A 185 LYS cc_start: 0.8973 (mttt) cc_final: 0.8631 (mtmm) REVERT: A 199 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7986 (mt-10) REVERT: A 266 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7702 (tpp) REVERT: B 90 GLU cc_start: 0.8429 (tt0) cc_final: 0.7911 (tm-30) REVERT: B 144 GLU cc_start: 0.7879 (tt0) cc_final: 0.7445 (tp30) REVERT: B 382 LYS cc_start: 0.8724 (tttt) cc_final: 0.8470 (tppp) REVERT: B 386 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8652 (mt-10) outliers start: 11 outliers final: 3 residues processed: 93 average time/residue: 0.6448 time to fit residues: 62.9305 Evaluate side-chains 83 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 15 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 0.3980 chunk 18 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.113345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.075817 restraints weight = 9270.461| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.80 r_work: 0.2698 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6968 Z= 0.154 Angle : 0.455 12.254 9370 Z= 0.234 Chirality : 0.039 0.140 956 Planarity : 0.003 0.040 1202 Dihedral : 3.720 14.690 902 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.54 % Allowed : 12.01 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.30), residues: 812 helix: 2.29 (0.25), residues: 442 sheet: -0.01 (0.50), residues: 92 loop : 1.11 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 77 TYR 0.013 0.001 TYR B 44 PHE 0.029 0.001 PHE A 273 TRP 0.006 0.001 TRP A 249 HIS 0.011 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6962) covalent geometry : angle 0.45507 ( 9370) hydrogen bonds : bond 0.03902 ( 363) hydrogen bonds : angle 4.00964 ( 1071) metal coordination : bond 0.02483 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.290 Fit side-chains REVERT: A 63 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8523 (ttm) REVERT: A 86 LYS cc_start: 0.8422 (tttt) cc_final: 0.8144 (tppt) REVERT: A 123 GLU cc_start: 0.9052 (tt0) cc_final: 0.8351 (tp30) REVERT: A 185 LYS cc_start: 0.9020 (mttt) cc_final: 0.8696 (mtmm) REVERT: A 199 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7959 (mt-10) REVERT: A 260 MET cc_start: 0.8035 (mmt) cc_final: 0.7232 (mmm) REVERT: A 266 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7765 (tpp) REVERT: B 71 ASP cc_start: 0.8511 (t0) cc_final: 0.8162 (t0) REVERT: B 90 GLU cc_start: 0.8447 (tt0) cc_final: 0.7910 (tm-30) REVERT: B 144 GLU cc_start: 0.7931 (tt0) cc_final: 0.7558 (tp30) REVERT: B 260 MET cc_start: 0.7989 (mmt) cc_final: 0.7669 (mmt) outliers start: 11 outliers final: 4 residues processed: 84 average time/residue: 0.6398 time to fit residues: 56.4711 Evaluate side-chains 75 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 294 GLN B 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.113768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.076155 restraints weight = 9574.854| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.84 r_work: 0.2671 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6968 Z= 0.149 Angle : 0.446 11.881 9370 Z= 0.229 Chirality : 0.039 0.140 956 Planarity : 0.003 0.029 1202 Dihedral : 3.688 14.784 902 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.68 % Allowed : 12.43 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.30), residues: 812 helix: 2.41 (0.25), residues: 438 sheet: -0.09 (0.51), residues: 92 loop : 1.19 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 19 TYR 0.012 0.001 TYR B 44 PHE 0.023 0.001 PHE B 273 TRP 0.006 0.001 TRP B 197 HIS 0.002 0.000 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6962) covalent geometry : angle 0.44621 ( 9370) hydrogen bonds : bond 0.03838 ( 363) hydrogen bonds : angle 3.95796 ( 1071) metal coordination : bond 0.00188 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.297 Fit side-chains REVERT: A 63 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8541 (ttm) REVERT: A 86 LYS cc_start: 0.8414 (tttt) cc_final: 0.8121 (tppt) REVERT: A 123 GLU cc_start: 0.9061 (tt0) cc_final: 0.8336 (tp30) REVERT: A 185 LYS cc_start: 0.8987 (mttt) cc_final: 0.8641 (mtmm) REVERT: A 199 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7926 (mt-10) REVERT: A 260 MET cc_start: 0.7930 (mmt) cc_final: 0.7197 (mmm) REVERT: A 266 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7754 (tpp) REVERT: B 63 MET cc_start: 0.9005 (ttm) cc_final: 0.8187 (ttp) REVERT: B 71 ASP cc_start: 0.8537 (t0) cc_final: 0.8200 (t0) REVERT: B 90 GLU cc_start: 0.8432 (tt0) cc_final: 0.7883 (tm-30) REVERT: B 144 GLU cc_start: 0.7972 (tt0) cc_final: 0.7597 (tp30) outliers start: 12 outliers final: 5 residues processed: 84 average time/residue: 0.6828 time to fit residues: 60.1187 Evaluate side-chains 77 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 294 GLN B 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.112292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.074400 restraints weight = 9730.945| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.86 r_work: 0.2642 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6968 Z= 0.193 Angle : 0.471 11.466 9370 Z= 0.244 Chirality : 0.040 0.170 956 Planarity : 0.003 0.031 1202 Dihedral : 3.755 15.653 902 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.96 % Allowed : 13.69 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.30), residues: 812 helix: 2.38 (0.25), residues: 438 sheet: -0.10 (0.52), residues: 92 loop : 1.09 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 417 TYR 0.014 0.001 TYR B 44 PHE 0.029 0.002 PHE A 273 TRP 0.006 0.001 TRP A 197 HIS 0.002 0.000 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 6962) covalent geometry : angle 0.47086 ( 9370) hydrogen bonds : bond 0.04103 ( 363) hydrogen bonds : angle 4.03474 ( 1071) metal coordination : bond 0.00257 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.297 Fit side-chains REVERT: A 63 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8542 (ttm) REVERT: A 86 LYS cc_start: 0.8416 (tttt) cc_final: 0.8090 (tppt) REVERT: A 123 GLU cc_start: 0.9059 (tt0) cc_final: 0.8311 (tp30) REVERT: A 185 LYS cc_start: 0.8998 (mttt) cc_final: 0.8650 (mtmm) REVERT: A 199 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 260 MET cc_start: 0.7869 (mmt) cc_final: 0.7131 (mmm) REVERT: A 266 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7812 (tpp) REVERT: B 63 MET cc_start: 0.9094 (ttm) cc_final: 0.8513 (ttp) REVERT: B 71 ASP cc_start: 0.8560 (t0) cc_final: 0.8250 (t0) REVERT: B 90 GLU cc_start: 0.8468 (tt0) cc_final: 0.7881 (tm-30) outliers start: 14 outliers final: 4 residues processed: 76 average time/residue: 0.7067 time to fit residues: 56.1574 Evaluate side-chains 72 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.074245 restraints weight = 9459.924| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.80 r_work: 0.2659 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6968 Z= 0.202 Angle : 0.475 10.978 9370 Z= 0.247 Chirality : 0.041 0.181 956 Planarity : 0.003 0.030 1202 Dihedral : 3.804 15.931 902 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.68 % Allowed : 13.69 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.30), residues: 812 helix: 2.36 (0.25), residues: 438 sheet: 0.37 (0.60), residues: 72 loop : 0.86 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 417 TYR 0.014 0.001 TYR B 44 PHE 0.011 0.002 PHE B 67 TRP 0.007 0.001 TRP B 197 HIS 0.002 0.000 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 6962) covalent geometry : angle 0.47464 ( 9370) hydrogen bonds : bond 0.04147 ( 363) hydrogen bonds : angle 4.05541 ( 1071) metal coordination : bond 0.00322 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.275 Fit side-chains REVERT: A 63 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8427 (tmm) REVERT: A 86 LYS cc_start: 0.8399 (tttt) cc_final: 0.8054 (tppt) REVERT: A 123 GLU cc_start: 0.9055 (tt0) cc_final: 0.8289 (tp30) REVERT: A 185 LYS cc_start: 0.9001 (mttt) cc_final: 0.8676 (mttp) REVERT: A 199 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7916 (mt-10) REVERT: A 266 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7822 (tpp) REVERT: B 90 GLU cc_start: 0.8470 (tt0) cc_final: 0.7875 (tm-30) REVERT: B 144 GLU cc_start: 0.7996 (tt0) cc_final: 0.7657 (tp30) REVERT: B 218 GLU cc_start: 0.8891 (tp30) cc_final: 0.8329 (tp30) REVERT: B 266 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.7555 (tpp) outliers start: 12 outliers final: 4 residues processed: 76 average time/residue: 0.7227 time to fit residues: 57.4105 Evaluate side-chains 73 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 266 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 17 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 236 ASN A 294 GLN B 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.114277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.076467 restraints weight = 9558.499| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.87 r_work: 0.2690 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6968 Z= 0.123 Angle : 0.449 10.637 9370 Z= 0.231 Chirality : 0.039 0.130 956 Planarity : 0.003 0.027 1202 Dihedral : 3.668 15.009 902 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.12 % Allowed : 14.25 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.30), residues: 812 helix: 2.42 (0.25), residues: 442 sheet: 0.31 (0.61), residues: 72 loop : 0.87 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 417 TYR 0.011 0.001 TYR B 111 PHE 0.032 0.001 PHE A 273 TRP 0.006 0.001 TRP B 197 HIS 0.002 0.000 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6962) covalent geometry : angle 0.44896 ( 9370) hydrogen bonds : bond 0.03604 ( 363) hydrogen bonds : angle 3.88872 ( 1071) metal coordination : bond 0.00305 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.182 Fit side-chains REVERT: A 66 ASN cc_start: 0.8301 (p0) cc_final: 0.7925 (p0) REVERT: A 86 LYS cc_start: 0.8352 (tttt) cc_final: 0.7994 (tppt) REVERT: A 123 GLU cc_start: 0.9059 (tt0) cc_final: 0.8322 (tp30) REVERT: A 185 LYS cc_start: 0.9007 (mttt) cc_final: 0.8697 (mttp) REVERT: A 199 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7929 (mt-10) REVERT: B 71 ASP cc_start: 0.8553 (t0) cc_final: 0.8187 (t0) REVERT: B 90 GLU cc_start: 0.8476 (tt0) cc_final: 0.7871 (tm-30) REVERT: B 144 GLU cc_start: 0.7964 (tt0) cc_final: 0.7636 (tp30) REVERT: B 218 GLU cc_start: 0.8940 (tp30) cc_final: 0.8332 (tp30) outliers start: 8 outliers final: 3 residues processed: 80 average time/residue: 0.6730 time to fit residues: 56.4081 Evaluate side-chains 75 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 15 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 294 GLN B 11 GLN B 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.111345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.073591 restraints weight = 9547.357| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.81 r_work: 0.2644 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.802 6968 Z= 0.755 Angle : 0.501 10.689 9370 Z= 0.261 Chirality : 0.041 0.147 956 Planarity : 0.003 0.026 1202 Dihedral : 3.815 16.779 902 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.12 % Allowed : 14.53 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.30), residues: 812 helix: 2.36 (0.25), residues: 438 sheet: 0.31 (0.61), residues: 72 loop : 0.81 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 417 TYR 0.015 0.001 TYR B 44 PHE 0.019 0.002 PHE B 273 TRP 0.007 0.001 TRP A 197 HIS 0.002 0.000 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 6962) covalent geometry : angle 0.50102 ( 9370) hydrogen bonds : bond 0.04261 ( 363) hydrogen bonds : angle 4.11076 ( 1071) metal coordination : bond 0.73586 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.310 Fit side-chains REVERT: A 86 LYS cc_start: 0.8377 (tttt) cc_final: 0.8025 (tppt) REVERT: A 123 GLU cc_start: 0.9061 (tt0) cc_final: 0.8320 (tp30) REVERT: A 185 LYS cc_start: 0.9015 (mttt) cc_final: 0.8697 (mttp) REVERT: A 199 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7899 (mt-10) REVERT: B 71 ASP cc_start: 0.8584 (t0) cc_final: 0.8221 (t0) REVERT: B 90 GLU cc_start: 0.8469 (tt0) cc_final: 0.7886 (tm-30) REVERT: B 144 GLU cc_start: 0.8029 (tt0) cc_final: 0.7731 (tp30) REVERT: B 218 GLU cc_start: 0.8903 (tp30) cc_final: 0.8302 (tp30) REVERT: B 266 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.7615 (tpp) outliers start: 8 outliers final: 5 residues processed: 72 average time/residue: 0.7469 time to fit residues: 56.1833 Evaluate side-chains 70 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 266 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 61 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN A 294 GLN B 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.076571 restraints weight = 9409.018| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.02 r_work: 0.2706 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 6968 Z= 0.130 Angle : 0.474 10.438 9370 Z= 0.247 Chirality : 0.039 0.128 956 Planarity : 0.003 0.036 1202 Dihedral : 3.709 15.534 902 Min Nonbonded Distance : 1.427 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.70 % Allowed : 15.08 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.30), residues: 812 helix: 2.46 (0.25), residues: 438 sheet: 0.20 (0.60), residues: 72 loop : 0.85 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 417 TYR 0.012 0.001 TYR B 111 PHE 0.031 0.001 PHE A 273 TRP 0.006 0.001 TRP B 204 HIS 0.022 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6962) covalent geometry : angle 0.47381 ( 9370) hydrogen bonds : bond 0.03647 ( 363) hydrogen bonds : angle 3.92198 ( 1071) metal coordination : bond 0.04631 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.322 Fit side-chains REVERT: A 66 ASN cc_start: 0.8295 (p0) cc_final: 0.7909 (p0) REVERT: A 86 LYS cc_start: 0.8360 (tttt) cc_final: 0.8027 (tppt) REVERT: A 123 GLU cc_start: 0.9062 (tt0) cc_final: 0.8316 (tp30) REVERT: A 185 LYS cc_start: 0.9001 (mttt) cc_final: 0.8693 (mttp) REVERT: A 199 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7908 (mt-10) REVERT: A 218 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8138 (mm-30) REVERT: B 63 MET cc_start: 0.9183 (ttm) cc_final: 0.8475 (ttp) REVERT: B 71 ASP cc_start: 0.8559 (t0) cc_final: 0.8187 (t0) REVERT: B 90 GLU cc_start: 0.8470 (tt0) cc_final: 0.7865 (tm-30) REVERT: B 218 GLU cc_start: 0.8925 (tp30) cc_final: 0.8303 (tp30) outliers start: 5 outliers final: 3 residues processed: 74 average time/residue: 0.7100 time to fit residues: 54.9887 Evaluate side-chains 72 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.0270 chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.077234 restraints weight = 9338.501| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.00 r_work: 0.2731 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 6968 Z= 0.131 Angle : 0.469 10.425 9370 Z= 0.244 Chirality : 0.039 0.136 956 Planarity : 0.003 0.040 1202 Dihedral : 3.664 15.152 902 Min Nonbonded Distance : 1.422 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.98 % Allowed : 14.94 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.45 (0.30), residues: 812 helix: 2.45 (0.25), residues: 442 sheet: 0.24 (0.61), residues: 72 loop : 0.85 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 417 TYR 0.011 0.001 TYR B 111 PHE 0.014 0.001 PHE B 273 TRP 0.005 0.001 TRP B 197 HIS 0.030 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6962) covalent geometry : angle 0.46912 ( 9370) hydrogen bonds : bond 0.03569 ( 363) hydrogen bonds : angle 3.86559 ( 1071) metal coordination : bond 0.04976 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2143.80 seconds wall clock time: 37 minutes 30.62 seconds (2250.62 seconds total)