Starting phenix.real_space_refine on Thu Jul 24 11:02:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h1j_34428/07_2025/8h1j_34428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h1j_34428/07_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_34428/07_2025/8h1j_34428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h1j_34428/07_2025/8h1j_34428.map" model { file = "/net/cci-nas-00/data/ceres_data/8h1j_34428/07_2025/8h1j_34428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h1j_34428/07_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-5711/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: 4.37, per 1000 atoms: 0.76 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: 2.05 Conformation dependent library (CDL) restraints added in 827.3 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: 2.68 Time building geometry restraints manager: 2.25 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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.730 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.110 ------------------------------------------------------------------------------- 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 : 0.419 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: 0.2859 time to fit residues: 23.5552 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 : 0.372 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138413 restraints weight = 8324.774| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.67 r_work: 0.3601 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- 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 : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7372 (mmtt) cc_final: 0.6750 (pttt) REVERT: A 121 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 207 LYS cc_start: 0.7802 (tptm) cc_final: 0.7523 (ttmt) REVERT: A 338 ASN cc_start: 0.6371 (p0) cc_final: 0.5884 (p0) outliers start: 13 outliers final: 7 residues processed: 44 average time/residue: 0.2739 time to fit residues: 14.6946 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 : 0.400 ------------------------------------------------------------------------------- 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: 10.0000 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.170621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132846 restraints weight = 8285.350| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.57 r_work: 0.3428 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 6171 Z= 0.345 Angle : 0.696 9.481 8958 Z= 0.365 Chirality : 0.043 0.273 1070 Planarity : 0.006 0.050 648 Dihedral : 23.108 97.339 2373 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.33 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: 1.51 (0.45), residues: 358 helix: 1.85 (0.38), residues: 175 sheet: -0.14 (0.63), residues: 75 loop : 0.64 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 141 HIS 0.005 0.002 HIS A 163 PHE 0.029 0.003 PHE A 35 TYR 0.025 0.003 TYR A 309 ARG 0.004 0.001 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.06880 ( 310) hydrogen bonds : angle 4.06916 ( 727) metal coordination : bond 0.00782 ( 4) metal coordination : angle 5.34604 ( 6) covalent geometry : bond 0.00745 ( 6167) covalent geometry : angle 0.68193 ( 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 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 20 LEU cc_start: 0.7748 (tp) cc_final: 0.7518 (tt) REVERT: A 48 LYS cc_start: 0.7761 (mmtt) cc_final: 0.6804 (pttt) REVERT: A 121 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8210 (mp10) REVERT: A 278 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6206 (pt0) REVERT: A 280 LEU cc_start: 0.6103 (pp) cc_final: 0.5896 (pt) REVERT: A 338 ASN cc_start: 0.6908 (p0) cc_final: 0.6590 (p0) outliers start: 12 outliers final: 8 residues processed: 43 average time/residue: 0.1940 time to fit residues: 10.8922 Evaluate side-chains 38 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.180596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143150 restraints weight = 8521.893| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.57 r_work: 0.3562 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6171 Z= 0.107 Angle : 0.449 4.553 8958 Z= 0.248 Chirality : 0.031 0.134 1070 Planarity : 0.003 0.045 648 Dihedral : 22.758 94.968 2370 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.57 % Allowed : 13.64 % 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: 2.22 (0.46), residues: 358 helix: 2.59 (0.38), residues: 175 sheet: 0.08 (0.65), residues: 75 loop : 0.77 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 349 HIS 0.002 0.000 HIS A 163 PHE 0.011 0.001 PHE A 35 TYR 0.016 0.001 TYR A 309 ARG 0.004 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 310) hydrogen bonds : angle 3.34953 ( 727) metal coordination : bond 0.00233 ( 4) metal coordination : angle 3.18047 ( 6) covalent geometry : bond 0.00222 ( 6167) covalent geometry : angle 0.44111 ( 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 44 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7413 (mmtt) cc_final: 0.6519 (pttt) REVERT: A 121 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7734 (mp10) REVERT: A 207 LYS cc_start: 0.7583 (tptm) cc_final: 0.7323 (ttmt) REVERT: A 278 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5778 (pt0) REVERT: A 329 GLN cc_start: 0.7946 (mt0) cc_final: 0.7519 (mm-40) outliers start: 11 outliers final: 8 residues processed: 44 average time/residue: 0.2279 time to fit residues: 14.0783 Evaluate side-chains 39 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 40.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.175797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139034 restraints weight = 8556.446| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.67 r_work: 0.3438 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2378 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= 0.205 Angle : 0.529 5.746 8958 Z= 0.287 Chirality : 0.035 0.200 1070 Planarity : 0.004 0.047 648 Dihedral : 22.839 96.816 2370 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.22 % Allowed : 13.96 % Favored : 81.82 % 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: 1.95 (0.46), residues: 358 helix: 2.37 (0.38), residues: 175 sheet: -0.10 (0.64), residues: 75 loop : 0.68 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 349 HIS 0.004 0.001 HIS A 166 PHE 0.025 0.002 PHE A 35 TYR 0.021 0.002 TYR A 309 ARG 0.002 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.05217 ( 310) hydrogen bonds : angle 3.59241 ( 727) metal coordination : bond 0.00353 ( 4) metal coordination : angle 3.07521 ( 6) covalent geometry : bond 0.00442 ( 6167) covalent geometry : angle 0.52322 ( 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 : 0.739 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7450 (mmtt) cc_final: 0.6874 (pttt) REVERT: A 121 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8000 (mp10) REVERT: A 278 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6393 (pt0) REVERT: A 280 LEU cc_start: 0.6127 (pp) cc_final: 0.5895 (pt) REVERT: A 329 GLN cc_start: 0.8460 (mt0) cc_final: 0.7709 (mm-40) outliers start: 13 outliers final: 10 residues processed: 40 average time/residue: 0.2401 time to fit residues: 13.4217 Evaluate side-chains 39 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 64 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.179491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143267 restraints weight = 8573.137| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.63 r_work: 0.3502 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2530 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= 0.120 Angle : 0.449 5.374 8958 Z= 0.247 Chirality : 0.031 0.144 1070 Planarity : 0.003 0.044 648 Dihedral : 22.711 95.400 2369 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.22 % Allowed : 13.96 % Favored : 81.82 % 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: 2.25 (0.46), residues: 358 helix: 2.73 (0.38), residues: 175 sheet: 0.11 (0.69), residues: 68 loop : 0.52 (0.60), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 349 HIS 0.003 0.001 HIS A 279 PHE 0.018 0.001 PHE A 35 TYR 0.019 0.001 TYR A 309 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 310) hydrogen bonds : angle 3.32056 ( 727) metal coordination : bond 0.00167 ( 4) metal coordination : angle 2.42269 ( 6) covalent geometry : bond 0.00254 ( 6167) covalent geometry : angle 0.44510 ( 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 40 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7316 (mmtt) cc_final: 0.6724 (pttt) REVERT: A 121 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: A 278 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6152 (pt0) REVERT: A 280 LEU cc_start: 0.6124 (pp) cc_final: 0.5860 (pt) REVERT: A 329 GLN cc_start: 0.8125 (mt0) cc_final: 0.7703 (mm-40) outliers start: 13 outliers final: 11 residues processed: 40 average time/residue: 0.3283 time to fit residues: 17.8821 Evaluate side-chains 38 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 58 GLU Chi-restraints excluded: chain A residue 64 GLN 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: 10.0000 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.174129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.136924 restraints weight = 8701.625| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.64 r_work: 0.3437 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6171 Z= 0.250 Angle : 0.570 6.220 8958 Z= 0.307 Chirality : 0.037 0.223 1070 Planarity : 0.004 0.046 648 Dihedral : 22.899 96.657 2369 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 1.60 (0.45), residues: 358 helix: 2.16 (0.38), residues: 176 sheet: -0.24 (0.63), residues: 73 loop : 0.30 (0.61), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 141 HIS 0.004 0.001 HIS A 166 PHE 0.025 0.002 PHE A 35 TYR 0.023 0.002 TYR A 309 ARG 0.002 0.001 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.05687 ( 310) hydrogen bonds : angle 3.65998 ( 727) metal coordination : bond 0.00450 ( 4) metal coordination : angle 2.66522 ( 6) covalent geometry : bond 0.00538 ( 6167) covalent geometry : angle 0.56600 ( 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: 14 poor density : 29 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7525 (mmtt) cc_final: 0.7039 (pttt) REVERT: A 121 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: A 278 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6487 (pt0) REVERT: A 329 GLN cc_start: 0.8423 (mt0) cc_final: 0.7653 (mm-40) outliers start: 14 outliers final: 10 residues processed: 43 average time/residue: 0.1490 time to fit residues: 9.0565 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 : 0.381 ------------------------------------------------------------------------------- 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 58 GLU 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: 0.0000 chunk 38 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 36 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.181085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139463 restraints weight = 8610.662| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.63 r_work: 0.3661 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6171 Z= 0.107 Angle : 0.444 6.150 8958 Z= 0.243 Chirality : 0.031 0.131 1070 Planarity : 0.003 0.046 648 Dihedral : 22.687 95.267 2369 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.55 % Allowed : 13.31 % Favored : 82.14 % 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: 2.08 (0.46), residues: 358 helix: 2.69 (0.38), residues: 175 sheet: -0.11 (0.67), residues: 70 loop : 0.36 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 349 HIS 0.004 0.001 HIS A 279 PHE 0.013 0.001 PHE A 35 TYR 0.018 0.001 TYR A 309 ARG 0.002 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 310) hydrogen bonds : angle 3.24418 ( 727) metal coordination : bond 0.00142 ( 4) metal coordination : angle 2.07947 ( 6) covalent geometry : bond 0.00224 ( 6167) covalent geometry : angle 0.44053 ( 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 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7306 (mmtt) cc_final: 0.6673 (pttt) REVERT: A 121 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8008 (mp10) REVERT: A 278 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.5882 (pt0) REVERT: A 329 GLN cc_start: 0.8433 (mt0) cc_final: 0.7657 (mm-40) outliers start: 14 outliers final: 10 residues processed: 43 average time/residue: 0.1841 time to fit residues: 10.9642 Evaluate side-chains 39 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.174891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136047 restraints weight = 8575.933| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.84 r_work: 0.3542 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6171 Z= 0.230 Angle : 0.563 7.755 8958 Z= 0.299 Chirality : 0.036 0.205 1070 Planarity : 0.004 0.046 648 Dihedral : 22.839 96.845 2369 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 1.44 (0.45), residues: 358 helix: 2.17 (0.38), residues: 176 sheet: -0.45 (0.63), residues: 72 loop : 0.08 (0.60), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 141 HIS 0.005 0.001 HIS A 166 PHE 0.024 0.002 PHE A 35 TYR 0.023 0.002 TYR A 309 ARG 0.002 0.000 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.05444 ( 310) hydrogen bonds : angle 3.58976 ( 727) metal coordination : bond 0.00447 ( 4) metal coordination : angle 4.92689 ( 6) covalent geometry : bond 0.00497 ( 6167) covalent geometry : angle 0.54864 ( 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 43 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7143 (OUTLIER) cc_final: 0.6895 (p0) REVERT: A 48 LYS cc_start: 0.7519 (mmtt) cc_final: 0.6957 (pttt) REVERT: A 121 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: A 278 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.5843 (pt0) REVERT: A 329 GLN cc_start: 0.8211 (mt0) cc_final: 0.7475 (mm-40) outliers start: 14 outliers final: 11 residues processed: 42 average time/residue: 0.1471 time to fit residues: 8.7745 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 : 0.415 ------------------------------------------------------------------------------- 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 58 GLU Chi-restraints excluded: chain A residue 64 GLN 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: 9.9990 chunk 33 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 overall best weight: 5.5986 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.174766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136227 restraints weight = 8676.898| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.90 r_work: 0.3535 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6171 Z= 0.235 Angle : 0.571 8.197 8958 Z= 0.303 Chirality : 0.036 0.209 1070 Planarity : 0.005 0.046 648 Dihedral : 22.849 96.234 2369 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.22 % Allowed : 14.94 % 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: 1.17 (0.45), residues: 358 helix: 2.01 (0.38), residues: 176 sheet: -0.87 (0.62), residues: 74 loop : 0.09 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.004 0.002 HIS A 166 PHE 0.026 0.002 PHE A 35 TYR 0.023 0.002 TYR A 309 ARG 0.002 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.05418 ( 310) hydrogen bonds : angle 3.62890 ( 727) metal coordination : bond 0.00393 ( 4) metal coordination : angle 3.75122 ( 6) covalent geometry : bond 0.00508 ( 6167) covalent geometry : angle 0.56320 ( 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 41 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7552 (mmtt) cc_final: 0.6958 (pttt) REVERT: A 121 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: A 278 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5890 (pt0) REVERT: A 329 GLN cc_start: 0.8364 (mt0) cc_final: 0.7533 (mm-40) outliers start: 13 outliers final: 11 residues processed: 40 average time/residue: 0.1716 time to fit residues: 9.5590 Evaluate side-chains 41 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 58 GLU Chi-restraints excluded: chain A residue 64 GLN 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: 3.9990 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 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: 1.9990 chunk 15 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.175951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.137314 restraints weight = 8662.566| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.87 r_work: 0.3553 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2900 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= 0.187 Angle : 0.535 8.114 8958 Z= 0.284 Chirality : 0.034 0.193 1070 Planarity : 0.004 0.046 648 Dihedral : 22.826 96.613 2369 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 1.37 (0.46), residues: 358 helix: 2.19 (0.38), residues: 176 sheet: -0.60 (0.64), residues: 72 loop : -0.02 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 349 HIS 0.004 0.001 HIS A 279 PHE 0.024 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 0.04995 ( 310) hydrogen bonds : angle 3.52755 ( 727) metal coordination : bond 0.00321 ( 4) metal coordination : angle 3.56911 ( 6) covalent geometry : bond 0.00404 ( 6167) covalent geometry : angle 0.52668 ( 8952) =============================================================================== Job complete usr+sys time: 3090.75 seconds wall clock time: 55 minutes 49.00 seconds (3349.00 seconds total)