Starting phenix.real_space_refine on Mon Feb 10 21:33:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwm_38738/02_2025/8xwm_38738.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwm_38738/02_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_38738/02_2025/8xwm_38738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwm_38738/02_2025/8xwm_38738.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwm_38738/02_2025/8xwm_38738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwm_38738/02_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-5592/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: 2.53, per 1000 atoms: 0.93 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: 0.80 Conformation dependent library (CDL) restraints added in 351.2 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: 0.29 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: 0.73 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: 0.600 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.490 Find NCS groups from input model: 0.020 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.140 ------------------------------------------------------------------------------- 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 : 0.329 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: 0.1117 time to fit residues: 13.7993 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 : 0.344 ------------------------------------------------------------------------------- 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 = 50)----------------| | 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 = 0.094828 restraints weight = 3639.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.095888 restraints weight = 2590.035| |-----------------------------------------------------------------------------| 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 : 0.302 Fit side-chains REVERT: D 9 GLU cc_start: 0.8526 (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: 0.1097 time to fit residues: 10.8934 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 : 0.322 ------------------------------------------------------------------------------- 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: 0.3980 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.0070 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 245 GLN R 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.118238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.092950 restraints weight = 6285.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095079 restraints weight = 3419.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096513 restraints weight = 2361.256| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2780 Z= 0.183 Angle : 0.532 5.032 3801 Z= 0.280 Chirality : 0.040 0.121 475 Planarity : 0.004 0.042 467 Dihedral : 3.935 15.829 391 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.42 % Allowed : 19.13 % Favored : 75.45 % 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 (0.45), residues: 359 helix: 2.27 (0.33), residues: 238 sheet: 0.30 (1.03), residues: 31 loop : -1.43 (0.64), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 112 HIS 0.002 0.000 HIS R 150 PHE 0.013 0.001 PHE D 32 TYR 0.013 0.001 TYR R 197 ARG 0.007 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: 15 poor density : 71 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: D 9 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7912 (mm-30) REVERT: R 141 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.8762 (p) REVERT: R 267 TYR cc_start: 0.8304 (t80) cc_final: 0.8042 (t80) REVERT: R 319 GLN cc_start: 0.8410 (tt0) cc_final: 0.7821 (tm-30) outliers start: 15 outliers final: 10 residues processed: 80 average time/residue: 0.0928 time to fit residues: 9.8068 Evaluate side-chains 76 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 262 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.118036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.093331 restraints weight = 6235.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.095482 restraints weight = 3465.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096852 restraints weight = 2394.775| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3523 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= 0.207 Angle : 0.543 4.964 3801 Z= 0.281 Chirality : 0.040 0.124 475 Planarity : 0.004 0.030 467 Dihedral : 3.805 15.335 391 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.42 % Allowed : 20.94 % Favored : 73.65 % 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: 1.80 (0.45), residues: 359 helix: 2.24 (0.33), residues: 240 sheet: 0.40 (1.05), residues: 31 loop : -1.57 (0.63), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.001 0.000 HIS R 150 PHE 0.011 0.001 PHE D 61 TYR 0.011 0.001 TYR R 197 ARG 0.005 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 80 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: D 9 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8018 (mm-30) REVERT: R 68 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8754 (mm) REVERT: R 267 TYR cc_start: 0.8304 (t80) cc_final: 0.8035 (t80) REVERT: R 277 MET cc_start: 0.8596 (ttm) cc_final: 0.8217 (ttm) REVERT: R 319 GLN cc_start: 0.8384 (tt0) cc_final: 0.7821 (tm-30) outliers start: 15 outliers final: 13 residues processed: 70 average time/residue: 0.0953 time to fit residues: 8.7657 Evaluate side-chains 80 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.119879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.096939 restraints weight = 6445.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098933 restraints weight = 3629.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.100025 restraints weight = 2527.845| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2780 Z= 0.187 Angle : 0.525 4.903 3801 Z= 0.272 Chirality : 0.040 0.125 475 Planarity : 0.003 0.030 467 Dihedral : 3.690 13.919 391 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 7.22 % Allowed : 21.30 % Favored : 71.48 % 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: 1.84 (0.46), residues: 359 helix: 2.24 (0.33), residues: 242 sheet: 0.53 (1.04), residues: 31 loop : -1.61 (0.63), 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 150 PHE 0.012 0.001 PHE D 32 TYR 0.009 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 84 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: R 123 SER cc_start: 0.8744 (m) cc_final: 0.8515 (t) REVERT: R 141 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8699 (p) REVERT: R 267 TYR cc_start: 0.8295 (t80) cc_final: 0.7896 (t80) REVERT: R 277 MET cc_start: 0.8569 (ttm) cc_final: 0.8157 (ttm) REVERT: R 319 GLN cc_start: 0.8314 (tt0) cc_final: 0.7836 (tm-30) outliers start: 20 outliers final: 15 residues processed: 72 average time/residue: 0.0793 time to fit residues: 7.8498 Evaluate side-chains 81 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 15 LEU Chi-restraints excluded: chain D residue 22 ASN 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 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 262 LEU Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.117401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.093838 restraints weight = 6511.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095818 restraints weight = 3696.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.097083 restraints weight = 2600.796| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2780 Z= 0.304 Angle : 0.638 12.478 3801 Z= 0.315 Chirality : 0.042 0.129 475 Planarity : 0.004 0.029 467 Dihedral : 3.837 14.059 391 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 7.22 % Allowed : 20.22 % 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: 1.77 (0.45), residues: 359 helix: 2.11 (0.33), residues: 240 sheet: 0.47 (1.04), residues: 31 loop : -1.26 (0.65), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 112 HIS 0.002 0.000 HIS R 323 PHE 0.015 0.002 PHE R 130 TYR 0.009 0.001 TYR R 197 ARG 0.002 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 87 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: R 277 MET cc_start: 0.8551 (ttm) cc_final: 0.8133 (ttm) REVERT: R 319 GLN cc_start: 0.8370 (tt0) cc_final: 0.7921 (tm-30) outliers start: 20 outliers final: 17 residues processed: 75 average time/residue: 0.0943 time to fit residues: 9.3352 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 : 0.306 ------------------------------------------------------------------------------- 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 15 LEU 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 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 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 262 LEU Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 0.0570 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 0.9902 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.119196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096187 restraints weight = 6692.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.098223 restraints weight = 3709.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.099543 restraints weight = 2597.626| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4073 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= 0.206 Angle : 0.594 10.326 3801 Z= 0.301 Chirality : 0.041 0.130 475 Planarity : 0.004 0.030 467 Dihedral : 3.697 13.542 391 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 6.86 % Allowed : 22.38 % 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: 1.80 (0.45), residues: 359 helix: 2.18 (0.33), residues: 242 sheet: 0.49 (1.05), residues: 31 loop : -1.51 (0.64), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 112 HIS 0.001 0.000 HIS R 242 PHE 0.013 0.001 PHE D 32 TYR 0.011 0.001 TYR R 197 ARG 0.002 0.000 ARG R 322 *********************** 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 82 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: R 123 SER cc_start: 0.8793 (m) cc_final: 0.8535 (t) REVERT: R 141 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8698 (p) REVERT: R 267 TYR cc_start: 0.8247 (t80) cc_final: 0.7904 (t80) REVERT: R 277 MET cc_start: 0.8567 (ttm) cc_final: 0.8135 (ttm) REVERT: R 319 GLN cc_start: 0.8354 (tt0) cc_final: 0.7878 (tm-30) outliers start: 19 outliers final: 17 residues processed: 70 average time/residue: 0.0764 time to fit residues: 7.3554 Evaluate side-chains 81 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 24 optimal weight: 0.0020 chunk 0 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.119986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096536 restraints weight = 6311.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.098700 restraints weight = 3518.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.099872 restraints weight = 2435.288| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4275 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= 0.180 Angle : 0.606 9.048 3801 Z= 0.303 Chirality : 0.041 0.164 475 Planarity : 0.004 0.030 467 Dihedral : 3.658 13.734 391 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.78 % Allowed : 23.10 % Favored : 71.12 % 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: 1.81 (0.46), residues: 359 helix: 2.18 (0.33), residues: 242 sheet: 0.46 (1.05), residues: 31 loop : -1.45 (0.65), 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 242 PHE 0.012 0.001 PHE R 59 TYR 0.009 0.001 TYR R 267 ARG 0.002 0.000 ARG R 288 *********************** 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 82 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: R 123 SER cc_start: 0.8755 (m) cc_final: 0.8497 (t) REVERT: R 141 SER cc_start: 0.9173 (OUTLIER) cc_final: 0.8706 (p) REVERT: R 267 TYR cc_start: 0.8313 (t80) cc_final: 0.7967 (t80) REVERT: R 277 MET cc_start: 0.8596 (ttm) cc_final: 0.8167 (ttm) REVERT: R 319 GLN cc_start: 0.8373 (tt0) cc_final: 0.7815 (tm-30) outliers start: 16 outliers final: 14 residues processed: 73 average time/residue: 0.0792 time to fit residues: 7.9244 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 : 0.319 ------------------------------------------------------------------------------- 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 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 237 THR 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: 0.5980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN R 290 ASN R 306 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.120571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097536 restraints weight = 6467.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099582 restraints weight = 3645.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100880 restraints weight = 2551.629| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4411 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= 0.182 Angle : 0.600 8.927 3801 Z= 0.299 Chirality : 0.042 0.217 475 Planarity : 0.003 0.031 467 Dihedral : 3.571 13.605 391 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 1.80 (0.45), residues: 359 helix: 2.20 (0.33), residues: 236 sheet: 0.48 (1.04), residues: 31 loop : -1.29 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 112 HIS 0.002 0.001 HIS R 306 PHE 0.011 0.001 PHE R 59 TYR 0.009 0.001 TYR R 267 ARG 0.001 0.000 ARG R 251 *********************** 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 84 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: R 123 SER cc_start: 0.8755 (m) cc_final: 0.8492 (t) REVERT: R 141 SER cc_start: 0.9176 (OUTLIER) cc_final: 0.8709 (p) REVERT: R 267 TYR cc_start: 0.8318 (t80) cc_final: 0.7936 (t80) REVERT: R 277 MET cc_start: 0.8600 (ttm) cc_final: 0.8213 (ttm) REVERT: R 319 GLN cc_start: 0.8343 (tt0) cc_final: 0.7850 (tm-30) outliers start: 19 outliers final: 17 residues processed: 74 average time/residue: 0.0793 time to fit residues: 8.0053 Evaluate side-chains 82 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain R residue 290 ASN 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 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.120366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096880 restraints weight = 6399.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.099057 restraints weight = 3559.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100394 restraints weight = 2448.703| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4455 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= 0.183 Angle : 0.609 10.646 3801 Z= 0.300 Chirality : 0.042 0.267 475 Planarity : 0.003 0.031 467 Dihedral : 3.517 13.551 391 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 6.50 % Allowed : 22.74 % 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: 1.89 (0.45), residues: 359 helix: 2.26 (0.33), residues: 236 sheet: 0.52 (1.04), residues: 31 loop : -1.24 (0.63), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 112 HIS 0.002 0.000 HIS R 306 PHE 0.012 0.001 PHE R 59 TYR 0.008 0.001 TYR R 267 ARG 0.002 0.000 ARG R 294 ********************** 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 82 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: R 123 SER cc_start: 0.8743 (m) cc_final: 0.8479 (t) REVERT: R 141 SER cc_start: 0.9175 (OUTLIER) cc_final: 0.8706 (p) REVERT: R 267 TYR cc_start: 0.8312 (t80) cc_final: 0.7932 (t80) REVERT: R 277 MET cc_start: 0.8609 (ttm) cc_final: 0.8199 (ttm) REVERT: R 319 GLN cc_start: 0.8315 (tt0) cc_final: 0.7852 (tm-30) outliers start: 18 outliers final: 17 residues processed: 72 average time/residue: 0.0798 time to fit residues: 7.8096 Evaluate side-chains 81 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain R residue 297 ASP Chi-restraints excluded: chain R residue 308 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.120957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.097475 restraints weight = 6273.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099591 restraints weight = 3504.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100915 restraints weight = 2435.828| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4541 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= 0.177 Angle : 0.600 10.367 3801 Z= 0.294 Chirality : 0.042 0.251 475 Planarity : 0.003 0.031 467 Dihedral : 3.463 13.615 391 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 6.14 % Allowed : 23.83 % Favored : 70.04 % 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 (0.45), residues: 359 helix: 2.28 (0.33), residues: 236 sheet: 0.57 (1.04), residues: 31 loop : -1.14 (0.64), residues: 92 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 0.009 0.001 TYR R 267 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: 1232.12 seconds wall clock time: 23 minutes 10.07 seconds (1390.07 seconds total)