Starting phenix.real_space_refine on Wed Mar 5 19:56:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwj_27756/03_2025/8dwj_27756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwj_27756/03_2025/8dwj_27756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dwj_27756/03_2025/8dwj_27756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwj_27756/03_2025/8dwj_27756.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwj_27756/03_2025/8dwj_27756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwj_27756/03_2025/8dwj_27756.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 14 5.49 5 S 13 5.16 5 C 1905 2.51 5 N 525 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3043 Number of models: 1 Model: "" Number of chains: 4 Chain: "P" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'GTP': 1} Classifications: {'RNA': 4, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3, None: 1} Not linked: pdbres="GTP P 1 " pdbres=" C P 2 " Chain: "T" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2781 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 24, 'TRANS': 314} 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 556 SG CYS A 37 35.483 27.676 19.865 1.00234.26 S ATOM 576 SG CYS A 40 35.253 23.162 19.878 1.00251.45 S ATOM 775 SG CYS A 65 36.508 25.850 23.034 1.00220.03 S ATOM 801 SG CYS A 68 38.485 25.430 20.056 1.00211.90 S Time building chain proxies: 3.28, per 1000 atoms: 1.08 Number of scatterers: 3043 At special positions: 0 Unit cell: (67.914, 67.914, 82.32, 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 13 16.00 P 14 15.00 O 585 8.00 N 525 7.00 C 1905 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 330.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 37 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 65 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 68 " Number of angles added : 6 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 642 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 4 sheets defined 38.9% alpha, 14.2% beta 3 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 Processing helix chain 'A' and resid 74 through 82 Processing helix chain 'A' and resid 82 through 97 removed outlier: 3.545A pdb=" N ARG A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.212A pdb=" N LYS A 151 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.522A pdb=" N ALA A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 297 Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.512A pdb=" N ILE A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 4.306A pdb=" N LYS A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126 Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 116 hydrogen bonds defined for protein. 306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 801 1.34 - 1.45: 621 1.45 - 1.57: 1675 1.57 - 1.69: 25 1.69 - 1.81: 20 Bond restraints: 3142 Sorted by residual: bond pdb=" N VAL A 232 " pdb=" CA VAL A 232 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.21e-02 6.83e+03 8.34e+00 bond pdb=" N ILE A 308 " pdb=" CA ILE A 308 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.21e-02 6.83e+03 8.01e+00 bond pdb=" N LYS A 300 " pdb=" CA LYS A 300 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.14e-02 7.69e+03 7.83e+00 bond pdb=" N ILE A 103 " pdb=" CA ILE A 103 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.56e+00 bond pdb=" N SER A 100 " pdb=" CA SER A 100 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.40e+00 ... (remaining 3137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 4121 2.27 - 4.54: 141 4.54 - 6.80: 20 6.80 - 9.07: 9 9.07 - 11.34: 6 Bond angle restraints: 4297 Sorted by residual: angle pdb=" N ARG A 87 " pdb=" CA ARG A 87 " pdb=" C ARG A 87 " ideal model delta sigma weight residual 110.97 105.46 5.51 1.09e+00 8.42e-01 2.55e+01 angle pdb=" CA LYS A 161 " pdb=" CB LYS A 161 " pdb=" CG LYS A 161 " ideal model delta sigma weight residual 114.10 122.41 -8.31 2.00e+00 2.50e-01 1.73e+01 angle pdb=" PB GTP P 1 " pdb=" O3B GTP P 1 " pdb=" PG GTP P 1 " ideal model delta sigma weight residual 120.50 131.84 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CB MET A 292 " pdb=" CG MET A 292 " pdb=" SD MET A 292 " ideal model delta sigma weight residual 112.70 123.89 -11.19 3.00e+00 1.11e-01 1.39e+01 angle pdb=" C TYR A 86 " pdb=" N ARG A 87 " pdb=" CA ARG A 87 " ideal model delta sigma weight residual 120.65 115.88 4.77 1.32e+00 5.74e-01 1.30e+01 ... (remaining 4292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 1660 17.58 - 35.16: 166 35.16 - 52.73: 44 52.73 - 70.31: 16 70.31 - 87.88: 7 Dihedral angle restraints: 1893 sinusoidal: 895 harmonic: 998 Sorted by residual: dihedral pdb=" C5' GTP P 1 " pdb=" O5' GTP P 1 " pdb=" PA GTP P 1 " pdb=" O3A GTP P 1 " ideal model delta sinusoidal sigma weight residual 69.27 143.55 -74.28 1 2.00e+01 2.50e-03 1.75e+01 dihedral pdb=" C8 GTP P 1 " pdb=" C1' GTP P 1 " pdb=" N9 GTP P 1 " pdb=" O4' GTP P 1 " ideal model delta sinusoidal sigma weight residual 104.59 42.71 61.88 1 2.00e+01 2.50e-03 1.27e+01 dihedral pdb=" CA GLU A 114 " pdb=" C GLU A 114 " pdb=" N LYS A 115 " pdb=" CA LYS A 115 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 1890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 274 0.040 - 0.079: 101 0.079 - 0.118: 44 0.118 - 0.158: 22 0.158 - 0.197: 10 Chirality restraints: 451 Sorted by residual: chirality pdb=" CA MET A 281 " pdb=" N MET A 281 " pdb=" C MET A 281 " pdb=" CB MET A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA LEU A 336 " pdb=" N LEU A 336 " pdb=" C LEU A 336 " pdb=" CB LEU A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA MET A 307 " pdb=" N MET A 307 " pdb=" C MET A 307 " pdb=" CB MET A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 448 not shown) Planarity restraints: 506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 145 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 146 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 203 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.58e+00 pdb=" N PRO A 204 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 314 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A 315 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " -0.032 5.00e-02 4.00e+02 ... (remaining 503 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 364 2.75 - 3.29: 2886 3.29 - 3.83: 5595 3.83 - 4.36: 6432 4.36 - 4.90: 10310 Nonbonded interactions: 25587 Sorted by model distance: nonbonded pdb=" OD1 ASP A 8 " pdb=" OH TYR A 89 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR A 55 " pdb=" OH TYR A 66 " model vdw 2.305 3.040 nonbonded pdb=" O LEU A 268 " pdb=" NE1 TRP A 294 " model vdw 2.370 3.120 nonbonded pdb=" NE2 GLN A 195 " pdb=" OG1 THR A 209 " model vdw 2.380 3.120 nonbonded pdb=" N ASP A 84 " pdb=" OD1 ASP A 84 " model vdw 2.384 3.120 ... (remaining 25582 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 group one per residue 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: 3.080 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.110 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5760 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 0.049 3142 Z= 0.340 Angle : 1.051 11.340 4297 Z= 0.584 Chirality : 0.059 0.197 451 Planarity : 0.008 0.064 506 Dihedral : 16.243 87.883 1251 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.33 % Allowed : 14.29 % Favored : 85.38 % 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: -2.71 (0.41), residues: 337 helix: -2.26 (0.37), residues: 116 sheet: -1.88 (0.68), residues: 51 loop : -1.29 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 266 HIS 0.002 0.001 HIS A 71 PHE 0.010 0.002 PHE A 293 TYR 0.015 0.002 TYR A 321 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TRP cc_start: 0.4145 (m100) cc_final: 0.3613 (m100) REVERT: A 87 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5065 (mtt180) REVERT: A 91 PHE cc_start: 0.6079 (t80) cc_final: 0.5870 (t80) REVERT: A 95 LYS cc_start: 0.7872 (tttt) cc_final: 0.6654 (mmmt) REVERT: A 137 ILE cc_start: 0.6298 (mm) cc_final: 0.5943 (tp) REVERT: A 147 LYS cc_start: 0.5333 (mmtt) cc_final: 0.5107 (tptt) REVERT: A 158 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6955 (mm-30) REVERT: A 176 SER cc_start: 0.4986 (m) cc_final: 0.4551 (p) REVERT: A 177 GLU cc_start: 0.6151 (tt0) cc_final: 0.5704 (mp0) REVERT: A 183 PRO cc_start: 0.5777 (Cg_exo) cc_final: 0.5370 (Cg_endo) REVERT: A 197 ARG cc_start: 0.5058 (tpt170) cc_final: 0.4838 (tpt170) REVERT: A 238 ASP cc_start: 0.6641 (m-30) cc_final: 0.6287 (t0) REVERT: A 258 VAL cc_start: 0.7790 (t) cc_final: 0.7587 (t) REVERT: A 264 ARG cc_start: 0.6642 (ptt180) cc_final: 0.6262 (ptt180) REVERT: A 266 TRP cc_start: 0.7664 (m100) cc_final: 0.7348 (m100) REVERT: A 267 VAL cc_start: 0.7865 (t) cc_final: 0.7545 (t) REVERT: A 279 LYS cc_start: 0.8305 (tttt) cc_final: 0.7956 (mtpp) REVERT: A 292 MET cc_start: 0.8457 (tmm) cc_final: 0.8071 (tpt) REVERT: A 322 MET cc_start: 0.7559 (mmt) cc_final: 0.7007 (ptp) REVERT: A 334 MET cc_start: 0.1537 (mmt) cc_final: 0.0137 (ttp) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.2077 time to fit residues: 23.1369 Evaluate side-chains 51 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 ASN ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.130523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.113253 restraints weight = 11641.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.114593 restraints weight = 7540.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.115453 restraints weight = 5624.887| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3142 Z= 0.252 Angle : 0.722 8.865 4297 Z= 0.371 Chirality : 0.048 0.179 451 Planarity : 0.007 0.056 506 Dihedral : 15.154 79.437 519 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.99 % Allowed : 16.61 % Favored : 81.40 % 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 (0.43), residues: 337 helix: -0.33 (0.47), residues: 109 sheet: -1.93 (0.70), residues: 52 loop : -0.86 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 294 HIS 0.005 0.001 HIS A 64 PHE 0.015 0.003 PHE A 241 TYR 0.011 0.002 TYR A 54 ARG 0.003 0.001 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7238 (tmt-80) cc_final: 0.4737 (mtt180) REVERT: A 95 LYS cc_start: 0.7300 (tttt) cc_final: 0.6725 (tppt) REVERT: A 176 SER cc_start: 0.4816 (m) cc_final: 0.4493 (p) REVERT: A 177 GLU cc_start: 0.6255 (tt0) cc_final: 0.4956 (mp0) REVERT: A 273 ARG cc_start: 0.3852 (mtt180) cc_final: 0.2243 (ttt180) outliers start: 6 outliers final: 2 residues processed: 54 average time/residue: 0.2217 time to fit residues: 13.8147 Evaluate side-chains 39 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 48 ASN ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.131266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.116767 restraints weight = 12411.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.116376 restraints weight = 10731.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.116612 restraints weight = 8432.165| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3142 Z= 0.165 Angle : 0.637 8.635 4297 Z= 0.321 Chirality : 0.045 0.140 451 Planarity : 0.006 0.050 506 Dihedral : 14.634 80.655 515 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.66 % Allowed : 17.61 % Favored : 79.73 % 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: -0.87 (0.45), residues: 337 helix: 0.46 (0.50), residues: 109 sheet: -1.63 (0.65), residues: 63 loop : -0.75 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 266 HIS 0.006 0.001 HIS A 134 PHE 0.013 0.002 PHE A 241 TYR 0.010 0.001 TYR A 213 ARG 0.002 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.630 Fit side-chains REVERT: A 25 VAL cc_start: 0.4859 (t) cc_final: 0.4632 (t) REVERT: A 87 ARG cc_start: 0.7194 (tmt-80) cc_final: 0.4790 (mtt180) REVERT: A 95 LYS cc_start: 0.6781 (tttt) cc_final: 0.6362 (mmmt) REVERT: A 176 SER cc_start: 0.5128 (m) cc_final: 0.4720 (p) REVERT: A 177 GLU cc_start: 0.5772 (tt0) cc_final: 0.4645 (mp0) REVERT: A 319 MET cc_start: 0.6184 (mpp) cc_final: 0.5980 (mpp) REVERT: A 334 MET cc_start: 0.2318 (mmt) cc_final: 0.0753 (ttp) outliers start: 8 outliers final: 3 residues processed: 48 average time/residue: 0.1882 time to fit residues: 10.8409 Evaluate side-chains 38 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 145 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.130431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.113272 restraints weight = 11575.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.114636 restraints weight = 7244.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.115571 restraints weight = 5494.301| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3142 Z= 0.184 Angle : 0.651 7.608 4297 Z= 0.330 Chirality : 0.045 0.145 451 Planarity : 0.006 0.051 506 Dihedral : 14.813 81.388 515 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.66 % Allowed : 19.93 % Favored : 78.41 % 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: -0.76 (0.45), residues: 337 helix: 0.66 (0.50), residues: 109 sheet: -1.52 (0.66), residues: 63 loop : -0.79 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 266 HIS 0.003 0.001 HIS A 134 PHE 0.013 0.002 PHE A 241 TYR 0.010 0.001 TYR A 213 ARG 0.002 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.349 Fit side-chains REVERT: A 87 ARG cc_start: 0.7297 (tmt-80) cc_final: 0.4814 (mtt180) REVERT: A 95 LYS cc_start: 0.7161 (tttt) cc_final: 0.6571 (mmmt) REVERT: A 176 SER cc_start: 0.5249 (m) cc_final: 0.4877 (p) REVERT: A 177 GLU cc_start: 0.5845 (tt0) cc_final: 0.4664 (mp0) REVERT: A 319 MET cc_start: 0.6324 (mpp) cc_final: 0.6047 (mpp) REVERT: A 334 MET cc_start: 0.2802 (OUTLIER) cc_final: 0.0998 (ttp) outliers start: 5 outliers final: 2 residues processed: 39 average time/residue: 0.2215 time to fit residues: 10.2003 Evaluate side-chains 36 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 17 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.128038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.112222 restraints weight = 12218.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.113325 restraints weight = 8297.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.114104 restraints weight = 6591.590| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3142 Z= 0.260 Angle : 0.725 8.182 4297 Z= 0.373 Chirality : 0.047 0.171 451 Planarity : 0.007 0.088 506 Dihedral : 15.543 85.116 515 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.65 % Allowed : 18.94 % Favored : 77.41 % 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: -1.38 (0.43), residues: 337 helix: 0.29 (0.47), residues: 112 sheet: -1.92 (0.61), residues: 63 loop : -1.28 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 150 HIS 0.005 0.002 HIS A 64 PHE 0.018 0.002 PHE A 11 TYR 0.013 0.002 TYR A 13 ARG 0.005 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.5205 (mtt180) REVERT: A 95 LYS cc_start: 0.7248 (tttt) cc_final: 0.6880 (tppt) REVERT: A 118 ILE cc_start: -0.1602 (OUTLIER) cc_final: -0.1969 (mt) REVERT: A 177 GLU cc_start: 0.5726 (tt0) cc_final: 0.4655 (mp0) REVERT: A 338 LYS cc_start: 0.6081 (mtmt) cc_final: 0.5688 (mtmt) outliers start: 11 outliers final: 5 residues processed: 43 average time/residue: 0.2091 time to fit residues: 10.5760 Evaluate side-chains 36 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 6 optimal weight: 0.0870 chunk 16 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.129352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.114157 restraints weight = 11824.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.114881 restraints weight = 8866.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.115064 restraints weight = 6882.337| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3142 Z= 0.186 Angle : 0.665 7.656 4297 Z= 0.336 Chirality : 0.046 0.143 451 Planarity : 0.006 0.053 506 Dihedral : 15.143 86.902 515 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.99 % Allowed : 20.27 % Favored : 75.75 % 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: -1.15 (0.43), residues: 337 helix: 0.57 (0.48), residues: 111 sheet: -1.64 (0.63), residues: 61 loop : -1.30 (0.44), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 266 HIS 0.002 0.001 HIS A 64 PHE 0.008 0.001 PHE A 31 TYR 0.008 0.001 TYR A 89 ARG 0.006 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.369 Fit side-chains REVERT: A 87 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.5130 (mtt180) REVERT: A 95 LYS cc_start: 0.7024 (tttt) cc_final: 0.6681 (tppt) REVERT: A 177 GLU cc_start: 0.5580 (tt0) cc_final: 0.4649 (mp0) REVERT: A 292 MET cc_start: 0.8020 (tmm) cc_final: 0.7651 (tmm) REVERT: A 331 MET cc_start: 0.3158 (mmt) cc_final: 0.2893 (mmt) REVERT: A 334 MET cc_start: 0.2913 (OUTLIER) cc_final: 0.1441 (ttp) outliers start: 12 outliers final: 3 residues processed: 45 average time/residue: 0.1871 time to fit residues: 10.1819 Evaluate side-chains 39 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.130102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.114090 restraints weight = 11674.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.115223 restraints weight = 8132.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.115659 restraints weight = 6554.491| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3142 Z= 0.189 Angle : 0.666 7.258 4297 Z= 0.334 Chirality : 0.047 0.209 451 Planarity : 0.006 0.051 506 Dihedral : 15.004 89.317 515 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.32 % Allowed : 21.26 % Favored : 75.42 % 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: -1.12 (0.44), residues: 337 helix: 0.73 (0.49), residues: 111 sheet: -1.67 (0.62), residues: 63 loop : -1.36 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 266 HIS 0.003 0.001 HIS A 64 PHE 0.013 0.002 PHE A 194 TYR 0.009 0.001 TYR A 54 ARG 0.007 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.5154 (mtt180) REVERT: A 95 LYS cc_start: 0.7069 (tttt) cc_final: 0.6695 (tppt) REVERT: A 292 MET cc_start: 0.8036 (tmm) cc_final: 0.7732 (tmm) REVERT: A 334 MET cc_start: 0.2830 (OUTLIER) cc_final: 0.1168 (ttp) outliers start: 10 outliers final: 5 residues processed: 44 average time/residue: 0.2025 time to fit residues: 10.7169 Evaluate side-chains 38 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 0.0370 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 0.0010 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 0.0670 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.131098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.117063 restraints weight = 11445.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.117346 restraints weight = 10491.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.117716 restraints weight = 7898.964| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5697 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3142 Z= 0.169 Angle : 0.679 12.772 4297 Z= 0.337 Chirality : 0.047 0.211 451 Planarity : 0.006 0.059 506 Dihedral : 14.622 89.461 515 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.99 % Allowed : 21.93 % Favored : 76.08 % 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: -0.98 (0.44), residues: 337 helix: 0.78 (0.50), residues: 112 sheet: -1.51 (0.65), residues: 58 loop : -1.31 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 150 HIS 0.003 0.001 HIS A 134 PHE 0.013 0.001 PHE A 194 TYR 0.007 0.001 TYR A 321 ARG 0.007 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 18 HIS cc_start: 0.6608 (m-70) cc_final: 0.6151 (p-80) REVERT: A 95 LYS cc_start: 0.6909 (tttt) cc_final: 0.6639 (tppt) REVERT: A 112 GLN cc_start: 0.1188 (OUTLIER) cc_final: 0.0854 (mm-40) REVERT: A 292 MET cc_start: 0.8061 (tmm) cc_final: 0.7755 (tmm) REVERT: A 334 MET cc_start: 0.2946 (OUTLIER) cc_final: 0.1106 (ttp) outliers start: 6 outliers final: 1 residues processed: 44 average time/residue: 0.1673 time to fit residues: 8.9220 Evaluate side-chains 34 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.130356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.113436 restraints weight = 12230.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.114832 restraints weight = 7955.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.115722 restraints weight = 6051.471| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3142 Z= 0.188 Angle : 0.688 10.974 4297 Z= 0.347 Chirality : 0.047 0.177 451 Planarity : 0.006 0.052 506 Dihedral : 14.513 89.022 515 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.00 % Allowed : 23.26 % Favored : 75.75 % 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: -0.93 (0.44), residues: 337 helix: 0.86 (0.50), residues: 110 sheet: -1.44 (0.62), residues: 64 loop : -1.27 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP A 150 HIS 0.003 0.001 HIS A 134 PHE 0.006 0.001 PHE A 81 TYR 0.009 0.001 TYR A 54 ARG 0.006 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.355 Fit side-chains REVERT: A 18 HIS cc_start: 0.6754 (m-70) cc_final: 0.6218 (p-80) REVERT: A 95 LYS cc_start: 0.7004 (tttt) cc_final: 0.6610 (tppt) REVERT: A 112 GLN cc_start: 0.0958 (OUTLIER) cc_final: 0.0706 (mm-40) REVERT: A 292 MET cc_start: 0.7996 (tmm) cc_final: 0.7708 (tmm) REVERT: A 334 MET cc_start: 0.2743 (OUTLIER) cc_final: 0.0834 (ttp) outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 0.1653 time to fit residues: 7.6726 Evaluate side-chains 35 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.130767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.114650 restraints weight = 12202.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.115521 restraints weight = 9122.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.116153 restraints weight = 7585.412| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3142 Z= 0.205 Angle : 0.683 10.469 4297 Z= 0.347 Chirality : 0.047 0.170 451 Planarity : 0.006 0.047 506 Dihedral : 14.412 89.664 515 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.33 % Allowed : 23.92 % Favored : 74.75 % 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: -1.03 (0.44), residues: 337 helix: 0.91 (0.50), residues: 110 sheet: -1.43 (0.61), residues: 64 loop : -1.48 (0.43), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 150 HIS 0.003 0.001 HIS A 64 PHE 0.012 0.001 PHE A 31 TYR 0.009 0.001 TYR A 54 ARG 0.005 0.000 ARG A 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.317 Fit side-chains REVERT: A 18 HIS cc_start: 0.6704 (m-70) cc_final: 0.6236 (p-80) REVERT: A 95 LYS cc_start: 0.7001 (tttt) cc_final: 0.6529 (mmmt) REVERT: A 292 MET cc_start: 0.8043 (tmm) cc_final: 0.7690 (tmm) REVERT: A 334 MET cc_start: 0.2793 (OUTLIER) cc_final: 0.1137 (ttp) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.1560 time to fit residues: 7.2649 Evaluate side-chains 37 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 25 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.0370 chunk 17 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.132200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.116900 restraints weight = 12289.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.117422 restraints weight = 8616.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.117095 restraints weight = 8065.368| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.6755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3142 Z= 0.177 Angle : 0.700 11.396 4297 Z= 0.357 Chirality : 0.046 0.212 451 Planarity : 0.005 0.048 506 Dihedral : 14.078 89.597 515 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.00 % Allowed : 24.92 % Favored : 74.09 % 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: -1.09 (0.43), residues: 337 helix: 0.69 (0.50), residues: 110 sheet: -1.41 (0.60), residues: 64 loop : -1.39 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 150 HIS 0.003 0.001 HIS A 134 PHE 0.013 0.001 PHE A 31 TYR 0.010 0.001 TYR A 139 ARG 0.006 0.000 ARG A 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1556.55 seconds wall clock time: 27 minutes 47.69 seconds (1667.69 seconds total)