Starting phenix.real_space_refine on Sat May 10 10:44:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h1j_34428/05_2025/8h1j_34428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h1j_34428/05_2025/8h1j_34428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h1j_34428/05_2025/8h1j_34428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h1j_34428/05_2025/8h1j_34428.map" model { file = "/net/cci-nas-00/data/ceres_data/8h1j_34428/05_2025/8h1j_34428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h1j_34428/05_2025/8h1j_34428.cif" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.134 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 Zn 1 6.06 5 P 134 5.49 5 S 6 5.16 5 C 3147 2.51 5 N 1063 2.21 5 O 1422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5773 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2930 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 1 Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "B" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2185 Classifications: {'RNA': 102} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 52, 'rna3p_pyr': 43} Link IDs: {'rna2p': 7, 'rna3p': 94} Chain breaks: 2 Chain: "D" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" 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 2567 SG CYS A 331 56.562 13.710 50.711 1.00192.35 S ATOM 2591 SG CYS A 334 56.015 10.341 49.439 1.00215.36 S ATOM 2728 SG CYS A 351 54.453 10.050 52.311 1.00222.37 S ATOM 2749 SG CYS A 354 57.190 11.215 52.766 1.00225.00 S Time building chain proxies: 4.21, per 1000 atoms: 0.73 Number of scatterers: 5773 At special positions: 0 Unit cell: (77.024, 102.256, 104.912, 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 S 6 16.00 P 134 15.00 O 1422 8.00 N 1063 7.00 C 3147 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: 1.57 Conformation dependent library (CDL) restraints added in 524.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 331 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 351 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 354 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 334 " Number of angles added : 6 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 674 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 4 sheets defined 48.6% alpha, 20.4% beta 57 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 14 through 47 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.857A pdb=" N LEU A 71 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 removed outlier: 3.711A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 232 Processing helix chain 'A' and resid 236 through 271 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 360 through 377 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.935A pdb=" N GLU A 116 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N LYS A 153 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU A 176 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A 155 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N GLU A 174 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL A 157 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU A 172 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 159 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER A 170 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ARG A 161 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU A 168 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 163 " --> pdb=" O HIS A 166 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 10 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS A 143 " --> pdb=" O TYR A 12 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 128 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.761A pdb=" N PHE A 186 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU A 278 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU A 273 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N SER A 319 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 275 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL A 321 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A 277 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 351 removed outlier: 3.918A pdb=" N TRP A 349 " --> pdb=" O HIS A 358 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1031 1.33 - 1.45: 2200 1.45 - 1.57: 2666 1.57 - 1.69: 263 1.69 - 1.81: 7 Bond restraints: 6167 Sorted by residual: bond pdb=" C1' G B -45 " pdb=" N9 G B -45 " ideal model delta sigma weight residual 1.475 1.455 0.020 1.50e-02 4.44e+03 1.78e+00 bond pdb=" O5' C B-107 " pdb=" C5' C B-107 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.64e+00 bond pdb=" N9 G B -45 " pdb=" C4 G B -45 " ideal model delta sigma weight residual 1.375 1.400 -0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" CB TRP A 313 " pdb=" CG TRP A 313 " ideal model delta sigma weight residual 1.498 1.461 0.037 3.10e-02 1.04e+03 1.41e+00 bond pdb=" C5 DC D -8 " pdb=" C6 DC D -8 " ideal model delta sigma weight residual 1.337 1.360 -0.023 2.00e-02 2.50e+03 1.37e+00 ... (remaining 6162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 8152 0.85 - 1.71: 663 1.71 - 2.56: 102 2.56 - 3.41: 26 3.41 - 4.27: 9 Bond angle restraints: 8952 Sorted by residual: angle pdb=" N VAL A 346 " pdb=" CA VAL A 346 " pdb=" C VAL A 346 " ideal model delta sigma weight residual 106.21 109.76 -3.55 1.07e+00 8.73e-01 1.10e+01 angle pdb=" O3' C B-107 " pdb=" C3' C B-107 " pdb=" C2' C B-107 " ideal model delta sigma weight residual 113.70 109.43 4.27 1.50e+00 4.44e-01 8.09e+00 angle pdb=" CA TYR A 309 " pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 113.90 118.12 -4.22 1.80e+00 3.09e-01 5.49e+00 angle pdb=" C HIS A 34 " pdb=" N PHE A 35 " pdb=" CA PHE A 35 " ideal model delta sigma weight residual 121.14 117.32 3.82 1.75e+00 3.27e-01 4.76e+00 angle pdb=" CA VAL A 346 " pdb=" C VAL A 346 " pdb=" O VAL A 346 " ideal model delta sigma weight residual 122.63 120.76 1.87 8.70e-01 1.32e+00 4.64e+00 ... (remaining 8947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 3010 18.12 - 36.25: 360 36.25 - 54.37: 229 54.37 - 72.49: 140 72.49 - 90.62: 27 Dihedral angle restraints: 3766 sinusoidal: 2717 harmonic: 1049 Sorted by residual: dihedral pdb=" CA PHE A 35 " pdb=" C PHE A 35 " pdb=" N LEU A 36 " pdb=" CA LEU A 36 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 dihedral pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" CB LEU A 222 " pdb=" CG LEU A 222 " ideal model delta sinusoidal sigma weight residual -180.00 -120.80 -59.20 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS A 143 " pdb=" CB LYS A 143 " pdb=" CG LYS A 143 " pdb=" CD LYS A 143 " ideal model delta sinusoidal sigma weight residual -60.00 -118.40 58.40 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 3763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 805 0.033 - 0.067: 201 0.067 - 0.100: 47 0.100 - 0.134: 13 0.134 - 0.167: 4 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C1' A B -88 " pdb=" O4' A B -88 " pdb=" C2' A B -88 " pdb=" N9 A B -88 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA PHE A 35 " pdb=" N PHE A 35 " pdb=" C PHE A 35 " pdb=" CB PHE A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" C3' C B-107 " pdb=" C4' C B-107 " pdb=" O3' C B-107 " pdb=" C2' C B-107 " both_signs ideal model delta sigma weight residual False -2.48 -2.62 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1067 not shown) Planarity restraints: 648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA C 21 " -0.029 2.00e-02 2.50e+03 1.26e-02 4.34e+00 pdb=" N9 DA C 21 " 0.005 2.00e-02 2.50e+03 pdb=" C8 DA C 21 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DA C 21 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DA C 21 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DA C 21 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA C 21 " -0.022 2.00e-02 2.50e+03 pdb=" N1 DA C 21 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA C 21 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA C 21 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA C 21 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -96 " -0.026 2.00e-02 2.50e+03 1.09e-02 3.58e+00 pdb=" N9 G B -96 " 0.025 2.00e-02 2.50e+03 pdb=" C8 G B -96 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B -96 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B -96 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B -96 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G B -96 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B -96 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G B -96 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B -96 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G B -96 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G B -96 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 106 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 107 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " 0.025 5.00e-02 4.00e+02 ... (remaining 645 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1045 2.77 - 3.30: 5147 3.30 - 3.83: 11172 3.83 - 4.37: 13054 4.37 - 4.90: 18820 Nonbonded interactions: 49238 Sorted by model distance: nonbonded pdb=" N2 G B-112 " pdb=" N6 A B -86 " model vdw 2.232 2.560 nonbonded pdb=" O2' G B-111 " pdb=" N4 C B -85 " model vdw 2.293 3.120 nonbonded pdb=" NH1 ARG A 270 " pdb=" OP1 A B -1 " model vdw 2.303 3.120 nonbonded pdb=" NH1 ARG A 110 " pdb=" OP1 C B 5 " model vdw 2.347 3.120 nonbonded pdb=" OG1 THR A 114 " pdb=" OP1 DA C 8 " model vdw 2.356 3.040 ... (remaining 49233 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.000 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.780 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 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 : 0.005 0.084 6171 Z= 0.229 Angle : 0.887 54.546 8958 Z= 0.332 Chirality : 0.034 0.167 1070 Planarity : 0.004 0.044 648 Dihedral : 22.060 90.616 3092 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.19 % Allowed : 9.74 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.19 (0.45), residues: 358 helix: 2.39 (0.37), residues: 173 sheet: 0.49 (0.60), residues: 81 loop : 0.79 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 349 HIS 0.005 0.001 HIS A 163 PHE 0.026 0.002 PHE A 35 TYR 0.024 0.002 TYR A 309 ARG 0.002 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.14264 ( 310) hydrogen bonds : angle 5.30813 ( 727) metal coordination : bond 0.04283 ( 4) metal coordination : angle 27.42998 ( 6) covalent geometry : bond 0.00476 ( 6167) covalent geometry : angle 0.53253 ( 8952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.6814 (tp) cc_final: 0.6588 (tt) REVERT: A 48 LYS cc_start: 0.7205 (mmtt) cc_final: 0.6282 (pttt) REVERT: A 58 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7176 (tt0) REVERT: A 95 ARG cc_start: 0.5955 (ttt90) cc_final: 0.5608 (ttp-110) REVERT: A 121 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: A 149 ASP cc_start: 0.7883 (m-30) cc_final: 0.7430 (t70) REVERT: A 175 VAL cc_start: 0.7996 (t) cc_final: 0.7731 (m) REVERT: A 205 ARG cc_start: 0.6711 (mtt180) cc_final: 0.6226 (mtm110) REVERT: A 207 LYS cc_start: 0.7279 (tptm) cc_final: 0.6720 (ttmt) REVERT: A 210 GLN cc_start: 0.8743 (pt0) cc_final: 0.8465 (pt0) REVERT: A 233 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5044 (mmtt) REVERT: A 245 LYS cc_start: 0.7923 (tttt) cc_final: 0.7696 (mttm) REVERT: A 248 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.7114 (tpt-90) REVERT: A 252 ARG cc_start: 0.6381 (mtt180) cc_final: 0.5898 (mtp-110) REVERT: A 349 TRP cc_start: 0.7735 (p-90) cc_final: 0.5851 (p-90) REVERT: A 367 ASN cc_start: 0.6759 (m-40) cc_final: 0.6497 (m-40) REVERT: A 371 GLU cc_start: 0.7470 (tp30) cc_final: 0.7177 (tp30) outliers start: 16 outliers final: 7 residues processed: 69 average time/residue: 0.2660 time to fit residues: 21.9868 Evaluate side-chains 44 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 341 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.0270 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.180414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138400 restraints weight = 8324.774| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.67 r_work: 0.3600 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6171 Z= 0.125 Angle : 0.512 13.572 8958 Z= 0.260 Chirality : 0.032 0.150 1070 Planarity : 0.004 0.042 648 Dihedral : 22.871 93.936 2380 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.22 % Allowed : 11.69 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.51 (0.46), residues: 358 helix: 2.68 (0.37), residues: 175 sheet: 0.68 (0.62), residues: 79 loop : 0.78 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 70 HIS 0.004 0.001 HIS A 163 PHE 0.017 0.001 PHE A 35 TYR 0.019 0.001 TYR A 309 ARG 0.004 0.000 ARG A 270 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 310) hydrogen bonds : angle 3.64617 ( 727) metal coordination : bond 0.01824 ( 4) metal coordination : angle 8.54336 ( 6) covalent geometry : bond 0.00257 ( 6167) covalent geometry : angle 0.46210 ( 8952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7366 (mmtt) cc_final: 0.6750 (pttt) REVERT: A 121 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: A 207 LYS cc_start: 0.7805 (tptm) cc_final: 0.7527 (ttmt) REVERT: A 338 ASN cc_start: 0.6372 (p0) cc_final: 0.5882 (p0) outliers start: 13 outliers final: 7 residues processed: 44 average time/residue: 0.2568 time to fit residues: 13.7756 Evaluate side-chains 31 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 317 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 33 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 166 HIS A 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.172194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134279 restraints weight = 8325.010| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.66 r_work: 0.3434 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 6171 Z= 0.303 Angle : 0.646 8.972 8958 Z= 0.342 Chirality : 0.040 0.255 1070 Planarity : 0.005 0.049 648 Dihedral : 23.034 96.648 2373 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.90 % Allowed : 12.66 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.69 (0.45), residues: 358 helix: 2.03 (0.38), residues: 175 sheet: -0.07 (0.63), residues: 75 loop : 0.70 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 70 HIS 0.005 0.001 HIS A 163 PHE 0.028 0.003 PHE A 35 TYR 0.025 0.002 TYR A 309 ARG 0.003 0.001 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.06435 ( 310) hydrogen bonds : angle 3.97000 ( 727) metal coordination : bond 0.00763 ( 4) metal coordination : angle 5.03562 ( 6) covalent geometry : bond 0.00657 ( 6167) covalent geometry : angle 0.63281 ( 8952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7671 (tp) cc_final: 0.7454 (tt) REVERT: A 48 LYS cc_start: 0.7776 (mmtt) cc_final: 0.6876 (pttt) REVERT: A 121 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8083 (mp10) REVERT: A 278 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6227 (pt0) REVERT: A 338 ASN cc_start: 0.6780 (p0) cc_final: 0.6503 (p0) outliers start: 12 outliers final: 9 residues processed: 42 average time/residue: 0.1941 time to fit residues: 10.6671 Evaluate side-chains 37 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.175326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136755 restraints weight = 8443.714| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.60 r_work: 0.3493 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6171 Z= 0.149 Angle : 0.489 5.891 8958 Z= 0.267 Chirality : 0.033 0.177 1070 Planarity : 0.004 0.047 648 Dihedral : 22.838 96.132 2370 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.90 % Allowed : 12.34 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.97 (0.46), residues: 358 helix: 2.35 (0.38), residues: 175 sheet: -0.05 (0.64), residues: 75 loop : 0.73 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 349 HIS 0.002 0.001 HIS A 166 PHE 0.020 0.002 PHE A 35 TYR 0.021 0.001 TYR A 309 ARG 0.003 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 310) hydrogen bonds : angle 3.54617 ( 727) metal coordination : bond 0.00329 ( 4) metal coordination : angle 3.48714 ( 6) covalent geometry : bond 0.00319 ( 6167) covalent geometry : angle 0.48062 ( 8952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7612 (mmtt) cc_final: 0.6811 (pttt) REVERT: A 121 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: A 278 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6044 (pt0) outliers start: 12 outliers final: 10 residues processed: 41 average time/residue: 0.1847 time to fit residues: 10.0624 Evaluate side-chains 41 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 31 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 40.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.175904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138181 restraints weight = 8323.148| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.57 r_work: 0.3487 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6171 Z= 0.163 Angle : 0.492 6.054 8958 Z= 0.269 Chirality : 0.033 0.180 1070 Planarity : 0.004 0.048 648 Dihedral : 22.802 96.070 2370 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.22 % Allowed : 12.34 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.02 (0.45), residues: 358 helix: 2.46 (0.38), residues: 175 sheet: 0.10 (0.65), residues: 73 loop : 0.51 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 349 HIS 0.004 0.001 HIS A 166 PHE 0.023 0.002 PHE A 35 TYR 0.021 0.001 TYR A 309 ARG 0.003 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 310) hydrogen bonds : angle 3.50343 ( 727) metal coordination : bond 0.00193 ( 4) metal coordination : angle 2.63399 ( 6) covalent geometry : bond 0.00351 ( 6167) covalent geometry : angle 0.48698 ( 8952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7519 (mmtt) cc_final: 0.6758 (pttt) REVERT: A 121 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: A 278 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.5905 (pt0) REVERT: A 280 LEU cc_start: 0.5855 (pp) cc_final: 0.5638 (pt) REVERT: A 329 GLN cc_start: 0.8027 (mt0) cc_final: 0.7435 (mm-40) outliers start: 13 outliers final: 11 residues processed: 40 average time/residue: 0.1573 time to fit residues: 8.7384 Evaluate side-chains 40 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.171897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134930 restraints weight = 8617.554| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.73 r_work: 0.3399 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 6171 Z= 0.333 Angle : 0.667 7.053 8958 Z= 0.355 Chirality : 0.042 0.267 1070 Planarity : 0.005 0.050 648 Dihedral : 23.114 97.840 2370 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.87 % Allowed : 12.34 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.44), residues: 358 helix: 1.67 (0.38), residues: 176 sheet: -0.53 (0.62), residues: 75 loop : 0.25 (0.59), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 141 HIS 0.007 0.002 HIS A 166 PHE 0.026 0.003 PHE A 35 TYR 0.025 0.003 TYR A 309 ARG 0.003 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.06762 ( 310) hydrogen bonds : angle 3.95159 ( 727) metal coordination : bond 0.00625 ( 4) metal coordination : angle 3.43380 ( 6) covalent geometry : bond 0.00720 ( 6167) covalent geometry : angle 0.66164 ( 8952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7666 (mmtt) cc_final: 0.7073 (pttt) REVERT: A 121 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: A 233 LYS cc_start: 0.7395 (pttt) cc_final: 0.6582 (mmtt) REVERT: A 278 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6429 (pt0) outliers start: 15 outliers final: 10 residues processed: 44 average time/residue: 0.1817 time to fit residues: 10.7234 Evaluate side-chains 41 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 31 optimal weight: 30.0000 chunk 48 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.176176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139609 restraints weight = 8738.181| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.72 r_work: 0.3459 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6171 Z= 0.181 Angle : 0.525 6.907 8958 Z= 0.283 Chirality : 0.035 0.194 1070 Planarity : 0.004 0.051 648 Dihedral : 22.960 96.529 2369 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.87 % Allowed : 12.66 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.45), residues: 358 helix: 2.07 (0.38), residues: 176 sheet: -0.41 (0.63), residues: 75 loop : 0.23 (0.60), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 349 HIS 0.004 0.001 HIS A 279 PHE 0.023 0.002 PHE A 35 TYR 0.022 0.002 TYR A 309 ARG 0.002 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04923 ( 310) hydrogen bonds : angle 3.58558 ( 727) metal coordination : bond 0.00273 ( 4) metal coordination : angle 2.46281 ( 6) covalent geometry : bond 0.00390 ( 6167) covalent geometry : angle 0.52135 ( 8952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7422 (mmtt) cc_final: 0.6674 (pttt) REVERT: A 121 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: A 278 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6085 (pt0) outliers start: 15 outliers final: 11 residues processed: 43 average time/residue: 0.1554 time to fit residues: 9.2926 Evaluate side-chains 36 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 overall best weight: 5.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.173668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136587 restraints weight = 8561.358| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.59 r_work: 0.3438 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6171 Z= 0.236 Angle : 0.579 7.054 8958 Z= 0.308 Chirality : 0.037 0.220 1070 Planarity : 0.005 0.051 648 Dihedral : 23.016 96.155 2369 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.55 % Allowed : 14.29 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.45), residues: 358 helix: 1.90 (0.38), residues: 176 sheet: -0.54 (0.62), residues: 73 loop : 0.03 (0.59), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 349 HIS 0.004 0.002 HIS A 166 PHE 0.024 0.002 PHE A 35 TYR 0.024 0.002 TYR A 309 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.05600 ( 310) hydrogen bonds : angle 3.74417 ( 727) metal coordination : bond 0.00403 ( 4) metal coordination : angle 4.46946 ( 6) covalent geometry : bond 0.00512 ( 6167) covalent geometry : angle 0.56767 ( 8952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.7295 (p0) REVERT: A 48 LYS cc_start: 0.7392 (mmtt) cc_final: 0.7032 (pttt) REVERT: A 121 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: A 233 LYS cc_start: 0.7421 (pttt) cc_final: 0.6602 (mmtt) REVERT: A 278 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6149 (pt0) REVERT: A 329 GLN cc_start: 0.8345 (mt0) cc_final: 0.7651 (mm-40) outliers start: 14 outliers final: 11 residues processed: 42 average time/residue: 0.1614 time to fit residues: 9.2674 Evaluate side-chains 40 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 36 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 overall best weight: 4.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.174566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138051 restraints weight = 8614.722| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.74 r_work: 0.3437 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6171 Z= 0.213 Angle : 0.546 6.057 8958 Z= 0.294 Chirality : 0.036 0.202 1070 Planarity : 0.004 0.051 648 Dihedral : 22.959 96.260 2369 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.55 % Allowed : 14.61 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.45), residues: 358 helix: 1.99 (0.38), residues: 176 sheet: -0.60 (0.62), residues: 73 loop : -0.00 (0.60), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 349 HIS 0.004 0.001 HIS A 166 PHE 0.023 0.002 PHE A 35 TYR 0.022 0.002 TYR A 309 ARG 0.002 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.05263 ( 310) hydrogen bonds : angle 3.61860 ( 727) metal coordination : bond 0.00273 ( 4) metal coordination : angle 3.27309 ( 6) covalent geometry : bond 0.00460 ( 6167) covalent geometry : angle 0.53995 ( 8952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7227 (p0) REVERT: A 48 LYS cc_start: 0.7402 (mmtt) cc_final: 0.6975 (pttt) REVERT: A 121 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: A 278 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6077 (pt0) REVERT: A 329 GLN cc_start: 0.8498 (mt0) cc_final: 0.7729 (mm-40) outliers start: 14 outliers final: 11 residues processed: 40 average time/residue: 0.1521 time to fit residues: 8.4180 Evaluate side-chains 39 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.172996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136157 restraints weight = 8638.599| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.63 r_work: 0.3431 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6171 Z= 0.243 Angle : 0.588 7.436 8958 Z= 0.314 Chirality : 0.037 0.227 1070 Planarity : 0.005 0.051 648 Dihedral : 23.068 96.465 2369 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.55 % Allowed : 14.94 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.45), residues: 358 helix: 1.88 (0.38), residues: 176 sheet: -0.84 (0.60), residues: 73 loop : -0.01 (0.61), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 349 HIS 0.007 0.002 HIS A 250 PHE 0.024 0.002 PHE A 35 TYR 0.024 0.002 TYR A 309 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.05841 ( 310) hydrogen bonds : angle 3.76635 ( 727) metal coordination : bond 0.00423 ( 4) metal coordination : angle 3.38645 ( 6) covalent geometry : bond 0.00528 ( 6167) covalent geometry : angle 0.58188 ( 8952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 716 Ramachandran restraints generated. 358 Oldfield, 0 Emsley, 358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7558 (OUTLIER) cc_final: 0.7335 (p0) REVERT: A 48 LYS cc_start: 0.7421 (mmtt) cc_final: 0.7005 (pttt) REVERT: A 121 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: A 233 LYS cc_start: 0.7412 (pttt) cc_final: 0.6608 (mmtt) REVERT: A 278 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6150 (pt0) REVERT: A 329 GLN cc_start: 0.8643 (mt0) cc_final: 0.7814 (mm-40) outliers start: 14 outliers final: 11 residues processed: 40 average time/residue: 0.1490 time to fit residues: 8.1312 Evaluate side-chains 40 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 331 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 36 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.175597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136470 restraints weight = 8644.162| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.76 r_work: 0.3548 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6171 Z= 0.193 Angle : 0.534 6.693 8958 Z= 0.286 Chirality : 0.035 0.194 1070 Planarity : 0.004 0.052 648 Dihedral : 22.977 96.361 2369 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.55 % Allowed : 14.94 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.45), residues: 358 helix: 2.08 (0.38), residues: 176 sheet: -0.75 (0.61), residues: 73 loop : -0.02 (0.61), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 349 HIS 0.005 0.002 HIS A 250 PHE 0.022 0.002 PHE A 35 TYR 0.022 0.002 TYR A 309 ARG 0.002 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.05170 ( 310) hydrogen bonds : angle 3.58950 ( 727) metal coordination : bond 0.00334 ( 4) metal coordination : angle 3.19890 ( 6) covalent geometry : bond 0.00418 ( 6167) covalent geometry : angle 0.52761 ( 8952) =============================================================================== Job complete usr+sys time: 2438.09 seconds wall clock time: 43 minutes 15.13 seconds (2595.13 seconds total)