Starting phenix.real_space_refine on Wed Mar 5 16:29:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwm_38738/03_2025/8xwm_38738.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwm_38738/03_2025/8xwm_38738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xwm_38738/03_2025/8xwm_38738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwm_38738/03_2025/8xwm_38738.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwm_38738/03_2025/8xwm_38738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwm_38738/03_2025/8xwm_38738.cif" } resolution = 3.71 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= 1.000 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 1787 2.51 5 N 461 2.21 5 O 454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 2722 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 414 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 59} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2308 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 288} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 2.35, per 1000 atoms: 0.86 Number of scatterers: 2722 At special positions: 0 Unit cell: (61.2125, 72.625, 93.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 454 8.00 N 461 7.00 C 1787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 12 " - pdb=" SG CYS D 38 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 54 " distance=2.03 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 308.7 milliseconds 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 694 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 2 sheets defined 70.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'R' and resid 44 through 76 removed outlier: 3.585A pdb=" N LYS R 48 " --> pdb=" O LEU R 44 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 115 through 149 Processing helix chain 'R' and resid 153 through 160 removed outlier: 3.898A pdb=" N THR R 156 " --> pdb=" O ARG R 153 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 183 Proline residue: R 179 - end of helix Processing helix chain 'R' and resid 203 through 213 removed outlier: 3.516A pdb=" N TRP R 207 " --> pdb=" O ASN R 203 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET R 209 " --> pdb=" O ALA R 205 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE R 213 " --> pdb=" O MET R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 240 Processing helix chain 'R' and resid 245 through 279 removed outlier: 3.915A pdb=" N ALA R 249 " --> pdb=" O GLN R 245 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 removed outlier: 3.578A pdb=" N ASP R 297 " --> pdb=" O ASP R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 329 removed outlier: 3.617A pdb=" N ARG R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 26 through 32 removed outlier: 4.200A pdb=" N VAL D 43 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 184 through 187 removed outlier: 3.794A pdb=" N ALA R 195 " --> pdb=" O VAL R 187 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.66 Time building geometry restraints manager: 0.86 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: 783 1.33 - 1.46: 519 1.46 - 1.58: 1451 1.58 - 1.70: 0 1.70 - 1.83: 27 Bond restraints: 2780 Sorted by residual: bond pdb=" CA ILE D 66 " pdb=" CB ILE D 66 " ideal model delta sigma weight residual 1.540 1.522 0.019 1.25e-02 6.40e+03 2.21e+00 bond pdb=" CA ILE D 26 " pdb=" CB ILE D 26 " ideal model delta sigma weight residual 1.537 1.521 0.016 1.25e-02 6.40e+03 1.64e+00 bond pdb=" CA VAL D 43 " pdb=" CB VAL D 43 " ideal model delta sigma weight residual 1.537 1.521 0.016 1.26e-02 6.30e+03 1.62e+00 bond pdb=" C ALA D 5 " pdb=" O ALA D 5 " ideal model delta sigma weight residual 1.231 1.212 0.019 2.00e-02 2.50e+03 9.32e-01 bond pdb=" N ALA D 5 " pdb=" CA ALA D 5 " ideal model delta sigma weight residual 1.458 1.476 -0.018 1.90e-02 2.77e+03 9.26e-01 ... (remaining 2775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 3553 0.95 - 1.90: 200 1.90 - 2.85: 26 2.85 - 3.80: 13 3.80 - 4.75: 9 Bond angle restraints: 3801 Sorted by residual: angle pdb=" C ALA D 5 " pdb=" N VAL D 6 " pdb=" CA VAL D 6 " ideal model delta sigma weight residual 122.75 118.66 4.09 1.45e+00 4.76e-01 7.98e+00 angle pdb=" CA VAL R 222 " pdb=" C VAL R 222 " pdb=" N PRO R 223 " ideal model delta sigma weight residual 120.83 119.35 1.48 6.10e-01 2.69e+00 5.89e+00 angle pdb=" CA ALA D 5 " pdb=" C ALA D 5 " pdb=" O ALA D 5 " ideal model delta sigma weight residual 120.80 117.01 3.79 1.70e+00 3.46e-01 4.98e+00 angle pdb=" N VAL R 222 " pdb=" CA VAL R 222 " pdb=" C VAL R 222 " ideal model delta sigma weight residual 112.35 109.75 2.60 1.20e+00 6.94e-01 4.70e+00 angle pdb=" C VAL R 222 " pdb=" CA VAL R 222 " pdb=" CB VAL R 222 " ideal model delta sigma weight residual 114.00 111.49 2.51 1.31e+00 5.83e-01 3.68e+00 ... (remaining 3796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 1489 17.99 - 35.99: 136 35.99 - 53.98: 20 53.98 - 71.97: 5 71.97 - 89.97: 2 Dihedral angle restraints: 1652 sinusoidal: 586 harmonic: 1066 Sorted by residual: dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual 93.00 65.65 27.35 1 1.00e+01 1.00e-02 1.07e+01 dihedral pdb=" CA LEU R 182 " pdb=" C LEU R 182 " pdb=" N PHE R 183 " pdb=" CA PHE R 183 " ideal model delta harmonic sigma weight residual -180.00 -164.42 -15.58 0 5.00e+00 4.00e-02 9.71e+00 dihedral pdb=" CA ARG R 153 " pdb=" CB ARG R 153 " pdb=" CG ARG R 153 " pdb=" CD ARG R 153 " ideal model delta sinusoidal sigma weight residual -60.00 -116.73 56.73 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 1649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 266 0.025 - 0.051: 127 0.051 - 0.076: 55 0.076 - 0.101: 19 0.101 - 0.127: 8 Chirality restraints: 475 Sorted by residual: chirality pdb=" CA ILE R 282 " pdb=" N ILE R 282 " pdb=" C ILE R 282 " pdb=" CB ILE R 282 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ALA D 5 " pdb=" N ALA D 5 " pdb=" C ALA D 5 " pdb=" CB ALA D 5 " both_signs ideal model delta sigma weight residual False 2.48 2.61 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA VAL D 21 " pdb=" N VAL D 21 " pdb=" C VAL D 21 " pdb=" CB VAL D 21 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 472 not shown) Planarity restraints: 467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 5 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C ALA D 5 " 0.025 2.00e-02 2.50e+03 pdb=" O ALA D 5 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL D 6 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 178 " 0.016 5.00e-02 4.00e+02 2.35e-02 8.81e-01 pdb=" N PRO R 179 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 179 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 179 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 119 " 0.004 2.00e-02 2.50e+03 7.20e-03 5.19e-01 pdb=" C CYS R 119 " -0.012 2.00e-02 2.50e+03 pdb=" O CYS R 119 " 0.005 2.00e-02 2.50e+03 pdb=" N LYS R 120 " 0.004 2.00e-02 2.50e+03 ... (remaining 464 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 502 2.77 - 3.30: 2718 3.30 - 3.83: 4376 3.83 - 4.37: 4544 4.37 - 4.90: 8397 Nonbonded interactions: 20537 Sorted by model distance: nonbonded pdb=" O ALA D 5 " pdb=" OG SER R 193 " model vdw 2.235 3.040 nonbonded pdb=" O ILE R 213 " pdb=" OG SER R 217 " model vdw 2.264 3.040 nonbonded pdb=" O GLY R 201 " pdb=" OG1 THR R 204 " model vdw 2.352 3.040 nonbonded pdb=" OE1 GLU R 198 " pdb=" NE ARG R 208 " model vdw 2.354 3.120 nonbonded pdb=" O CYS D 12 " pdb=" NH2 ARG R 289 " model vdw 2.492 3.120 ... (remaining 20532 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.770 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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 : 0.003 0.028 2780 Z= 0.204 Angle : 0.553 4.754 3801 Z= 0.323 Chirality : 0.038 0.127 475 Planarity : 0.003 0.024 467 Dihedral : 14.008 89.967 946 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.36 % Allowed : 10.11 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.46), residues: 359 helix: 2.12 (0.35), residues: 238 sheet: 0.27 (1.03), residues: 31 loop : -1.35 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 112 HIS 0.001 0.000 HIS R 150 PHE 0.008 0.001 PHE R 233 TYR 0.004 0.001 TYR R 231 ARG 0.003 0.000 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.279 Fit side-chains REVERT: D 9 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8163 (mm-30) REVERT: D 53 VAL cc_start: 0.8605 (m) cc_final: 0.8202 (m) REVERT: R 141 SER cc_start: 0.9067 (t) cc_final: 0.8603 (p) REVERT: R 188 TYR cc_start: 0.8462 (m-80) cc_final: 0.8199 (m-10) REVERT: R 245 GLN cc_start: 0.8201 (mp10) cc_final: 0.7898 (tt0) REVERT: R 267 TYR cc_start: 0.8266 (t80) cc_final: 0.7526 (t80) REVERT: R 277 MET cc_start: 0.8803 (ttp) cc_final: 0.8504 (ttm) REVERT: R 319 GLN cc_start: 0.8430 (tt0) cc_final: 0.7692 (tm-30) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.0977 time to fit residues: 12.1890 Evaluate side-chains 73 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN R 89 ASN R 129 ASN R 202 ASN R 203 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.116845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092849 restraints weight = 6358.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.094822 restraints weight = 3644.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.095882 restraints weight = 2592.993| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 2780 Z= 0.367 Angle : 0.655 7.570 3801 Z= 0.331 Chirality : 0.044 0.124 475 Planarity : 0.005 0.052 467 Dihedral : 3.982 15.020 391 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.78 % Allowed : 14.44 % Favored : 79.78 % 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: 1.40 (0.45), residues: 359 helix: 1.93 (0.33), residues: 239 sheet: 0.21 (1.00), residues: 31 loop : -1.63 (0.62), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.002 0.001 HIS R 323 PHE 0.014 0.002 PHE R 114 TYR 0.014 0.001 TYR R 197 ARG 0.003 0.001 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.342 Fit side-chains REVERT: D 9 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8189 (mm-30) REVERT: R 267 TYR cc_start: 0.8280 (t80) cc_final: 0.7896 (t80) REVERT: R 319 GLN cc_start: 0.8297 (tt0) cc_final: 0.7862 (tm-30) outliers start: 16 outliers final: 12 residues processed: 79 average time/residue: 0.1099 time to fit residues: 10.9696 Evaluate side-chains 74 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.115954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.091211 restraints weight = 6299.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093377 restraints weight = 3440.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.094701 restraints weight = 2339.862| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2780 Z= 0.278 Angle : 0.582 5.670 3801 Z= 0.303 Chirality : 0.041 0.122 475 Planarity : 0.005 0.042 467 Dihedral : 4.052 16.426 391 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 6.14 % Allowed : 19.49 % Favored : 74.37 % 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: 1.58 (0.45), residues: 359 helix: 2.09 (0.33), residues: 237 sheet: 0.18 (1.02), residues: 31 loop : -1.49 (0.64), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 112 HIS 0.002 0.001 HIS R 150 PHE 0.013 0.002 PHE D 32 TYR 0.013 0.001 TYR R 197 ARG 0.011 0.001 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: D 9 GLU cc_start: 0.8603 (mm-30) cc_final: 0.7993 (mm-30) REVERT: R 267 TYR cc_start: 0.8349 (t80) cc_final: 0.7964 (t80) REVERT: R 319 GLN cc_start: 0.8443 (tt0) cc_final: 0.7859 (tm-30) outliers start: 17 outliers final: 15 residues processed: 78 average time/residue: 0.0952 time to fit residues: 9.8157 Evaluate side-chains 80 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN R 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.116840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.091801 restraints weight = 6241.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.094008 restraints weight = 3428.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095332 restraints weight = 2357.171| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2780 Z= 0.223 Angle : 0.539 4.932 3801 Z= 0.282 Chirality : 0.040 0.125 475 Planarity : 0.004 0.030 467 Dihedral : 3.851 13.715 391 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 6.14 % Allowed : 21.30 % Favored : 72.56 % 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: 1.74 (0.45), residues: 359 helix: 2.20 (0.33), residues: 240 sheet: 0.33 (1.03), residues: 31 loop : -1.58 (0.63), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.002 0.000 HIS R 150 PHE 0.011 0.001 PHE D 61 TYR 0.012 0.001 TYR R 197 ARG 0.004 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: D 9 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8016 (mm-30) REVERT: D 16 ARG cc_start: 0.6555 (mtp-110) cc_final: 0.6236 (mtp180) REVERT: R 267 TYR cc_start: 0.8331 (t80) cc_final: 0.7949 (t80) REVERT: R 277 MET cc_start: 0.8521 (ttm) cc_final: 0.8179 (ttm) REVERT: R 319 GLN cc_start: 0.8431 (tt0) cc_final: 0.7834 (tm-30) outliers start: 17 outliers final: 14 residues processed: 73 average time/residue: 0.0909 time to fit residues: 8.8004 Evaluate side-chains 81 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 1 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 GLN R 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.117148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.093601 restraints weight = 6468.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.095591 restraints weight = 3646.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.096706 restraints weight = 2589.875| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2780 Z= 0.294 Angle : 0.576 6.135 3801 Z= 0.298 Chirality : 0.041 0.127 475 Planarity : 0.004 0.029 467 Dihedral : 3.899 14.542 391 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 7.94 % Allowed : 21.30 % Favored : 70.76 % 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: 1.68 (0.45), residues: 359 helix: 2.08 (0.33), residues: 240 sheet: 0.29 (1.05), residues: 31 loop : -1.34 (0.65), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.002 0.001 HIS R 150 PHE 0.013 0.002 PHE R 130 TYR 0.010 0.001 TYR R 197 ARG 0.004 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: D 16 ARG cc_start: 0.6630 (mtp-110) cc_final: 0.6245 (mtp180) REVERT: R 68 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8796 (mm) REVERT: R 277 MET cc_start: 0.8461 (ttm) cc_final: 0.8205 (ttm) REVERT: R 319 GLN cc_start: 0.8342 (tt0) cc_final: 0.7847 (tm-30) outliers start: 22 outliers final: 18 residues processed: 74 average time/residue: 0.0886 time to fit residues: 8.6355 Evaluate side-chains 81 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 216 GLN Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 308 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 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 = 0.3744 r_free = 0.3744 target = 0.118412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095355 restraints weight = 6560.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.097369 restraints weight = 3720.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098607 restraints weight = 2608.259| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2780 Z= 0.220 Angle : 0.556 5.141 3801 Z= 0.291 Chirality : 0.040 0.127 475 Planarity : 0.004 0.031 467 Dihedral : 3.804 13.762 391 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 6.86 % Allowed : 22.74 % Favored : 70.40 % 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: 1.70 (0.45), residues: 359 helix: 2.13 (0.33), residues: 242 sheet: 0.34 (1.06), residues: 31 loop : -1.58 (0.63), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.002 0.000 HIS R 150 PHE 0.011 0.001 PHE R 130 TYR 0.011 0.001 TYR R 197 ARG 0.003 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: D 16 ARG cc_start: 0.6645 (mtp-110) cc_final: 0.6237 (mtp180) REVERT: R 267 TYR cc_start: 0.8292 (t80) cc_final: 0.7964 (t80) REVERT: R 277 MET cc_start: 0.8445 (ttm) cc_final: 0.8202 (ttm) REVERT: R 319 GLN cc_start: 0.8327 (tt0) cc_final: 0.7831 (tm-30) outliers start: 19 outliers final: 17 residues processed: 70 average time/residue: 0.0886 time to fit residues: 8.2676 Evaluate side-chains 77 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 308 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 17 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.119989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.096955 restraints weight = 6740.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098889 restraints weight = 3701.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.100286 restraints weight = 2587.116| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2780 Z= 0.171 Angle : 0.545 6.392 3801 Z= 0.277 Chirality : 0.040 0.140 475 Planarity : 0.003 0.032 467 Dihedral : 3.655 13.820 391 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.42 % Allowed : 24.91 % Favored : 69.68 % 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: 1.92 (0.46), residues: 359 helix: 2.29 (0.33), residues: 242 sheet: 0.53 (1.08), residues: 31 loop : -1.52 (0.65), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.001 0.000 HIS R 242 PHE 0.013 0.001 PHE D 32 TYR 0.009 0.001 TYR R 197 ARG 0.002 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: R 123 SER cc_start: 0.8797 (m) cc_final: 0.8527 (t) REVERT: R 267 TYR cc_start: 0.8297 (t80) cc_final: 0.7941 (t80) REVERT: R 277 MET cc_start: 0.8496 (ttm) cc_final: 0.8104 (ttm) REVERT: R 319 GLN cc_start: 0.8354 (tt0) cc_final: 0.7839 (tm-30) outliers start: 15 outliers final: 13 residues processed: 75 average time/residue: 0.0878 time to fit residues: 8.7213 Evaluate side-chains 76 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.118821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095195 restraints weight = 6372.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.097335 restraints weight = 3552.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.098509 restraints weight = 2465.563| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2780 Z= 0.226 Angle : 0.583 5.892 3801 Z= 0.295 Chirality : 0.042 0.152 475 Planarity : 0.004 0.031 467 Dihedral : 3.643 13.121 391 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.78 % Allowed : 24.91 % Favored : 69.31 % 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: 1.83 (0.46), residues: 359 helix: 2.23 (0.33), residues: 242 sheet: 0.47 (1.07), residues: 31 loop : -1.58 (0.65), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.001 0.000 HIS R 242 PHE 0.010 0.001 PHE R 130 TYR 0.008 0.001 TYR R 197 ARG 0.003 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: D 16 ARG cc_start: 0.6873 (mtp-110) cc_final: 0.6651 (mtp-110) REVERT: R 94 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7793 (t0) REVERT: R 123 SER cc_start: 0.8759 (m) cc_final: 0.8534 (t) REVERT: R 267 TYR cc_start: 0.8349 (t80) cc_final: 0.7883 (t80) REVERT: R 277 MET cc_start: 0.8525 (ttm) cc_final: 0.8129 (ttm) REVERT: R 319 GLN cc_start: 0.8374 (tt0) cc_final: 0.7852 (tm-30) outliers start: 16 outliers final: 14 residues processed: 70 average time/residue: 0.0902 time to fit residues: 8.4201 Evaluate side-chains 79 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.0020 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.120264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.097076 restraints weight = 6463.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099137 restraints weight = 3632.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.100449 restraints weight = 2538.745| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2780 Z= 0.176 Angle : 0.580 10.093 3801 Z= 0.290 Chirality : 0.042 0.243 475 Planarity : 0.003 0.032 467 Dihedral : 3.571 13.792 391 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.05 % Allowed : 25.99 % Favored : 68.95 % 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: 1.91 (0.46), residues: 359 helix: 2.28 (0.33), residues: 242 sheet: 0.45 (1.06), residues: 31 loop : -1.45 (0.65), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 112 HIS 0.002 0.000 HIS R 242 PHE 0.012 0.001 PHE R 59 TYR 0.008 0.001 TYR R 197 ARG 0.001 0.000 ARG R 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: R 123 SER cc_start: 0.8772 (m) cc_final: 0.8547 (t) REVERT: R 267 TYR cc_start: 0.8345 (t80) cc_final: 0.7968 (t80) REVERT: R 277 MET cc_start: 0.8517 (ttm) cc_final: 0.8076 (ttm) REVERT: R 319 GLN cc_start: 0.8345 (tt0) cc_final: 0.7877 (tm-30) outliers start: 14 outliers final: 13 residues processed: 72 average time/residue: 0.0912 time to fit residues: 8.6165 Evaluate side-chains 75 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.119339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095431 restraints weight = 6406.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.097622 restraints weight = 3561.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.098976 restraints weight = 2461.631| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2780 Z= 0.198 Angle : 0.591 10.524 3801 Z= 0.292 Chirality : 0.043 0.284 475 Planarity : 0.003 0.032 467 Dihedral : 3.540 13.252 391 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.05 % Allowed : 25.27 % Favored : 69.68 % 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: 1.91 (0.46), residues: 359 helix: 2.27 (0.33), residues: 242 sheet: 0.45 (1.05), residues: 31 loop : -1.43 (0.64), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 112 HIS 0.001 0.000 HIS R 150 PHE 0.012 0.001 PHE R 59 TYR 0.007 0.001 TYR R 197 ARG 0.001 0.000 ARG R 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 718 Ramachandran restraints generated. 359 Oldfield, 0 Emsley, 359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: R 94 ASP cc_start: 0.7543 (t0) cc_final: 0.7064 (t0) REVERT: R 123 SER cc_start: 0.8798 (m) cc_final: 0.8547 (t) REVERT: R 267 TYR cc_start: 0.8350 (t80) cc_final: 0.8019 (t80) REVERT: R 277 MET cc_start: 0.8541 (ttm) cc_final: 0.8103 (ttm) REVERT: R 319 GLN cc_start: 0.8356 (tt0) cc_final: 0.7916 (tm-30) outliers start: 14 outliers final: 14 residues processed: 69 average time/residue: 0.0763 time to fit residues: 7.2517 Evaluate side-chains 76 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 286 CYS Chi-restraints excluded: chain R residue 297 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 18 optimal weight: 0.0170 chunk 10 optimal weight: 3.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.120396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.097187 restraints weight = 6396.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099253 restraints weight = 3633.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.100385 restraints weight = 2553.255| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2780 Z= 0.181 Angle : 0.585 10.665 3801 Z= 0.288 Chirality : 0.042 0.282 475 Planarity : 0.003 0.032 467 Dihedral : 3.527 13.680 391 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.78 % Allowed : 24.55 % Favored : 69.68 % 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: 359 helix: 2.31 (0.33), residues: 242 sheet: 0.45 (1.04), residues: 31 loop : -1.42 (0.64), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 112 HIS 0.001 0.000 HIS R 150 PHE 0.013 0.001 PHE D 32 TYR 0.007 0.001 TYR R 197 ARG 0.001 0.000 ARG R 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1207.94 seconds wall clock time: 21 minutes 42.82 seconds (1302.82 seconds total)