Starting phenix.real_space_refine on Wed Jul 23 10:44:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s15_24794/07_2025/7s15_24794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s15_24794/07_2025/7s15_24794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s15_24794/07_2025/7s15_24794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s15_24794/07_2025/7s15_24794.map" model { file = "/net/cci-nas-00/data/ceres_data/7s15_24794/07_2025/7s15_24794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s15_24794/07_2025/7s15_24794.cif" } resolution = 3.8 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= 0.060 sd= 0.638 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: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 2117 2.51 5 N 525 2.21 5 O 545 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3207 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3164 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 2 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'82L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.42, per 1000 atoms: 0.75 Number of scatterers: 3207 At special positions: 0 Unit cell: (65.296, 65.296, 114.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 F 2 9.00 O 545 8.00 N 525 7.00 C 2117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.04 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.05 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 0.82 Conformation dependent library (CDL) restraints added in 341.8 milliseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 66.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'R' and resid 31 through 52 removed outlier: 3.649A pdb=" N ARG R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 95 Processing helix chain 'R' and resid 138 through 166 removed outlier: 4.021A pdb=" N LEU R 142 " --> pdb=" O GLU R 138 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL R 160 " --> pdb=" O PHE R 156 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 202 removed outlier: 3.925A pdb=" N ALA R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER R 186 " --> pdb=" O ASN R 182 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE R 187 " --> pdb=" O LEU R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 221 Processing helix chain 'R' and resid 225 through 254 removed outlier: 3.698A pdb=" N TYR R 241 " --> pdb=" O VAL R 237 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU R 244 " --> pdb=" O ASN R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 276 removed outlier: 3.518A pdb=" N SER R 271 " --> pdb=" O ARG R 267 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 280 Processing helix chain 'R' and resid 281 through 292 removed outlier: 4.083A pdb=" N LEU R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 335 removed outlier: 4.182A pdb=" N ARG R 310 " --> pdb=" O TRP R 306 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 360 removed outlier: 4.333A pdb=" N LYS R 351 " --> pdb=" O CYS R 347 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER R 352 " --> pdb=" O ARG R 348 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR R 355 " --> pdb=" O LYS R 351 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 371 removed outlier: 3.894A pdb=" N PHE R 367 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 393 removed outlier: 4.098A pdb=" N PHE R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 404 removed outlier: 3.932A pdb=" N VAL R 398 " --> pdb=" O GLN R 394 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA R 399 " --> pdb=" O GLY R 395 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE R 404 " --> pdb=" O ILE R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 421 removed outlier: 3.663A pdb=" N GLN R 410 " --> pdb=" O ASN R 406 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE R 413 " --> pdb=" O VAL R 409 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU R 418 " --> pdb=" O ARG R 414 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG R 419 " --> pdb=" O LYS R 415 " (cutoff:3.500A) 162 hydrogen bonds defined for protein. 477 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: 0.67 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 972 1.34 - 1.46: 936 1.46 - 1.58: 1378 1.58 - 1.70: 0 1.70 - 1.82: 23 Bond restraints: 3309 Sorted by residual: bond pdb=" C41 82L R 501 " pdb=" O43 82L R 501 " ideal model delta sigma weight residual 1.259 1.303 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C12 82L R 501 " pdb=" C41 82L R 501 " ideal model delta sigma weight residual 1.527 1.485 0.042 2.00e-02 2.50e+03 4.35e+00 bond pdb=" C41 82L R 501 " pdb=" O42 82L R 501 " ideal model delta sigma weight residual 1.258 1.222 0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" CA GLN R 394 " pdb=" C GLN R 394 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.80e-02 3.09e+03 1.97e+00 bond pdb=" C1 82L R 501 " pdb=" C2 82L R 501 " ideal model delta sigma weight residual 1.523 1.498 0.025 2.00e-02 2.50e+03 1.59e+00 ... (remaining 3304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 4207 1.49 - 2.98: 253 2.98 - 4.47: 37 4.47 - 5.96: 10 5.96 - 7.45: 4 Bond angle restraints: 4511 Sorted by residual: angle pdb=" CA LEU R 166 " pdb=" C LEU R 166 " pdb=" N LEU R 167 " ideal model delta sigma weight residual 118.27 123.59 -5.32 1.59e+00 3.96e-01 1.12e+01 angle pdb=" CA CYS R 126 " pdb=" CB CYS R 126 " pdb=" SG CYS R 126 " ideal model delta sigma weight residual 114.40 121.85 -7.45 2.30e+00 1.89e-01 1.05e+01 angle pdb=" C ILE R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.92 117.03 4.89 1.73e+00 3.34e-01 7.99e+00 angle pdb=" N THR R 65 " pdb=" CA THR R 65 " pdb=" C THR R 65 " ideal model delta sigma weight residual 108.34 111.87 -3.53 1.31e+00 5.83e-01 7.27e+00 angle pdb=" CA TYR R 145 " pdb=" CB TYR R 145 " pdb=" CG TYR R 145 " ideal model delta sigma weight residual 113.90 109.74 4.16 1.80e+00 3.09e-01 5.34e+00 ... (remaining 4506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 1635 16.43 - 32.86: 209 32.86 - 49.30: 59 49.30 - 65.73: 9 65.73 - 82.16: 5 Dihedral angle restraints: 1917 sinusoidal: 786 harmonic: 1131 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -14.81 -71.19 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 153.24 -60.24 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CA CYS R 296 " pdb=" C CYS R 296 " pdb=" N TRP R 297 " pdb=" CA TRP R 297 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 1914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 272 0.034 - 0.069: 150 0.069 - 0.103: 49 0.103 - 0.137: 14 0.137 - 0.171: 1 Chirality restraints: 486 Sorted by residual: chirality pdb=" C22 82L R 501 " pdb=" C21 82L R 501 " pdb=" C23 82L R 501 " pdb=" C25 82L R 501 " both_signs ideal model delta sigma weight residual False 2.48 2.65 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CG LEU R 218 " pdb=" CB LEU R 218 " pdb=" CD1 LEU R 218 " pdb=" CD2 LEU R 218 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA GLN R 394 " pdb=" N GLN R 394 " pdb=" C GLN R 394 " pdb=" CB GLN R 394 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 483 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C32 82L R 501 " 0.315 2.00e-02 2.50e+03 1.43e-01 4.59e+02 pdb=" C33 82L R 501 " -0.165 2.00e-02 2.50e+03 pdb=" C34 82L R 501 " -0.149 2.00e-02 2.50e+03 pdb=" C35 82L R 501 " -0.048 2.00e-02 2.50e+03 pdb=" C36 82L R 501 " 0.036 2.00e-02 2.50e+03 pdb=" C37 82L R 501 " 0.022 2.00e-02 2.50e+03 pdb=" C38 82L R 501 " -0.078 2.00e-02 2.50e+03 pdb=" F39 82L R 501 " -0.074 2.00e-02 2.50e+03 pdb=" F40 82L R 501 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 82L R 501 " -0.066 2.00e-02 2.50e+03 3.87e-02 3.00e+01 pdb=" C25 82L R 501 " 0.041 2.00e-02 2.50e+03 pdb=" C26 82L R 501 " 0.021 2.00e-02 2.50e+03 pdb=" C27 82L R 501 " -0.014 2.00e-02 2.50e+03 pdb=" C28 82L R 501 " -0.025 2.00e-02 2.50e+03 pdb=" C29 82L R 501 " 0.015 2.00e-02 2.50e+03 pdb=" N30 82L R 501 " 0.059 2.00e-02 2.50e+03 pdb=" O31 82L R 501 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 82L R 501 " 0.022 2.00e-02 2.50e+03 2.15e-02 1.39e+01 pdb=" C11 82L R 501 " 0.013 2.00e-02 2.50e+03 pdb=" C12 82L R 501 " -0.009 2.00e-02 2.50e+03 pdb=" C13 82L R 501 " -0.026 2.00e-02 2.50e+03 pdb=" C14 82L R 501 " -0.007 2.00e-02 2.50e+03 pdb=" C15 82L R 501 " 0.019 2.00e-02 2.50e+03 pdb=" C17 82L R 501 " 0.016 2.00e-02 2.50e+03 pdb=" C18 82L R 501 " -0.049 2.00e-02 2.50e+03 pdb=" C41 82L R 501 " -0.009 2.00e-02 2.50e+03 pdb=" C8 82L R 501 " -0.011 2.00e-02 2.50e+03 pdb=" N16 82L R 501 " 0.022 2.00e-02 2.50e+03 pdb=" N9 82L R 501 " 0.017 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 204 2.72 - 3.26: 3555 3.26 - 3.81: 5083 3.81 - 4.35: 5892 4.35 - 4.90: 9473 Nonbonded interactions: 24207 Sorted by model distance: nonbonded pdb=" OH TYR R 241 " pdb=" OE2 GLU R 364 " model vdw 2.174 3.040 nonbonded pdb=" O GLN R 47 " pdb=" OG1 THR R 51 " model vdw 2.276 3.040 nonbonded pdb=" O THR R 386 " pdb=" OG SER R 389 " model vdw 2.293 3.040 nonbonded pdb=" O LEU R 349 " pdb=" OG SER R 352 " model vdw 2.317 3.040 nonbonded pdb=" OD1 ASN R 304 " pdb=" NE1 TRP R 306 " model vdw 2.326 3.120 ... (remaining 24202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.006 0.044 3313 Z= 0.276 Angle : 0.812 7.447 4519 Z= 0.443 Chirality : 0.046 0.171 486 Planarity : 0.008 0.143 551 Dihedral : 15.907 82.158 1173 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % 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: -4.51 (0.35), residues: 376 helix: -2.23 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -4.38 (0.42), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 297 HIS 0.003 0.001 HIS R 173 PHE 0.016 0.002 PHE R 143 TYR 0.015 0.002 TYR R 145 ARG 0.008 0.001 ARG R 64 Details of bonding type rmsd hydrogen bonds : bond 0.13309 ( 162) hydrogen bonds : angle 5.81600 ( 477) SS BOND : bond 0.01017 ( 4) SS BOND : angle 1.70485 ( 8) covalent geometry : bond 0.00618 ( 3309) covalent geometry : angle 0.80924 ( 4511) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 244 LEU cc_start: 0.9031 (mp) cc_final: 0.8820 (mp) REVERT: R 269 TYR cc_start: 0.8017 (m-10) cc_final: 0.7458 (m-80) REVERT: R 394 GLN cc_start: 0.9370 (pp30) cc_final: 0.8430 (pp30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1591 time to fit residues: 18.0427 Evaluate side-chains 66 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN R 180 HIS R 221 GLN R 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.123830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.108575 restraints weight = 8856.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.111768 restraints weight = 4506.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.113791 restraints weight = 2670.216| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3313 Z= 0.165 Angle : 0.723 7.064 4519 Z= 0.366 Chirality : 0.043 0.149 486 Planarity : 0.004 0.044 551 Dihedral : 6.204 27.861 455 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.45 % Favored : 92.29 % Rotamer: Outliers : 2.92 % Allowed : 19.30 % Favored : 77.78 % 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: -2.53 (0.42), residues: 376 helix: -0.74 (0.33), residues: 248 sheet: None (None), residues: 0 loop : -3.52 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 297 HIS 0.003 0.001 HIS R 363 PHE 0.011 0.001 PHE R 315 TYR 0.017 0.002 TYR R 235 ARG 0.005 0.001 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 162) hydrogen bonds : angle 4.35269 ( 477) SS BOND : bond 0.00751 ( 4) SS BOND : angle 1.54843 ( 8) covalent geometry : bond 0.00364 ( 3309) covalent geometry : angle 0.72113 ( 4511) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 34 GLU cc_start: 0.9068 (mp0) cc_final: 0.8830 (mp0) REVERT: R 198 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.7791 (t0) REVERT: R 234 GLN cc_start: 0.9363 (mm-40) cc_final: 0.8902 (mm110) REVERT: R 269 TYR cc_start: 0.8140 (m-10) cc_final: 0.7558 (m-80) REVERT: R 394 GLN cc_start: 0.9149 (pp30) cc_final: 0.8880 (pp30) REVERT: R 404 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5628 (m-80) outliers start: 10 outliers final: 5 residues processed: 83 average time/residue: 0.1263 time to fit residues: 13.1556 Evaluate side-chains 75 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 221 GLN Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 33 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.126914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.111280 restraints weight = 8572.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.114451 restraints weight = 4467.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.116523 restraints weight = 2701.144| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3313 Z= 0.124 Angle : 0.650 7.289 4519 Z= 0.325 Chirality : 0.040 0.114 486 Planarity : 0.004 0.049 551 Dihedral : 6.054 27.872 455 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.92 % Allowed : 23.10 % Favored : 73.98 % 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: -1.55 (0.44), residues: 376 helix: 0.01 (0.33), residues: 246 sheet: None (None), residues: 0 loop : -3.09 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 243 HIS 0.002 0.001 HIS R 99 PHE 0.010 0.001 PHE R 315 TYR 0.017 0.002 TYR R 145 ARG 0.003 0.000 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 162) hydrogen bonds : angle 3.78160 ( 477) SS BOND : bond 0.00699 ( 4) SS BOND : angle 1.68919 ( 8) covalent geometry : bond 0.00263 ( 3309) covalent geometry : angle 0.64647 ( 4511) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 68 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8648 (mm-30) REVERT: R 198 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8192 (t0) REVERT: R 284 TRP cc_start: 0.8873 (t60) cc_final: 0.8667 (t-100) REVERT: R 288 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8717 (mmtm) REVERT: R 394 GLN cc_start: 0.9088 (pp30) cc_final: 0.8776 (pp30) REVERT: R 404 PHE cc_start: 0.6167 (OUTLIER) cc_final: 0.5688 (m-80) outliers start: 10 outliers final: 5 residues processed: 86 average time/residue: 0.1260 time to fit residues: 13.7360 Evaluate side-chains 77 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 180 HIS R 300 ASN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.122049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.107550 restraints weight = 8780.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.110579 restraints weight = 4364.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.112568 restraints weight = 2568.406| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3313 Z= 0.205 Angle : 0.706 6.608 4519 Z= 0.359 Chirality : 0.042 0.120 486 Planarity : 0.005 0.054 551 Dihedral : 6.517 38.501 455 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 5.85 % Allowed : 22.81 % Favored : 71.35 % 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: -1.59 (0.44), residues: 376 helix: -0.03 (0.33), residues: 252 sheet: None (None), residues: 0 loop : -3.22 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 297 HIS 0.003 0.001 HIS R 173 PHE 0.010 0.001 PHE R 315 TYR 0.028 0.002 TYR R 148 ARG 0.004 0.001 ARG R 421 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 162) hydrogen bonds : angle 4.06444 ( 477) SS BOND : bond 0.00674 ( 4) SS BOND : angle 1.60196 ( 8) covalent geometry : bond 0.00461 ( 3309) covalent geometry : angle 0.70363 ( 4511) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: R 34 GLU cc_start: 0.8994 (mp0) cc_final: 0.8688 (mp0) REVERT: R 68 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8327 (mm-30) REVERT: R 284 TRP cc_start: 0.8919 (t60) cc_final: 0.8682 (t-100) REVERT: R 394 GLN cc_start: 0.9200 (pp30) cc_final: 0.8897 (pp30) REVERT: R 404 PHE cc_start: 0.6109 (OUTLIER) cc_final: 0.5594 (m-80) outliers start: 20 outliers final: 13 residues processed: 75 average time/residue: 0.1265 time to fit residues: 12.0232 Evaluate side-chains 80 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.124453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.109365 restraints weight = 8785.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.112480 restraints weight = 4440.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114527 restraints weight = 2646.509| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3313 Z= 0.143 Angle : 0.646 5.814 4519 Z= 0.328 Chirality : 0.041 0.116 486 Planarity : 0.004 0.043 551 Dihedral : 6.227 35.817 455 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 5.26 % Allowed : 24.27 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.44), residues: 376 helix: 0.14 (0.33), residues: 252 sheet: None (None), residues: 0 loop : -3.06 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 243 HIS 0.002 0.001 HIS R 363 PHE 0.010 0.001 PHE R 315 TYR 0.013 0.001 TYR R 145 ARG 0.003 0.000 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 162) hydrogen bonds : angle 3.78600 ( 477) SS BOND : bond 0.00594 ( 4) SS BOND : angle 1.30472 ( 8) covalent geometry : bond 0.00326 ( 3309) covalent geometry : angle 0.64469 ( 4511) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: R 34 GLU cc_start: 0.9017 (mp0) cc_final: 0.8773 (mp0) REVERT: R 269 TYR cc_start: 0.8212 (m-10) cc_final: 0.7702 (m-80) REVERT: R 284 TRP cc_start: 0.8804 (t60) cc_final: 0.8499 (t-100) REVERT: R 394 GLN cc_start: 0.9131 (pp30) cc_final: 0.8830 (pp30) REVERT: R 404 PHE cc_start: 0.6150 (OUTLIER) cc_final: 0.5586 (m-80) outliers start: 18 outliers final: 12 residues processed: 82 average time/residue: 0.1074 time to fit residues: 11.4939 Evaluate side-chains 79 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 0.0970 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.125658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.110462 restraints weight = 8796.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.113614 restraints weight = 4415.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.115635 restraints weight = 2635.148| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3313 Z= 0.121 Angle : 0.646 8.301 4519 Z= 0.319 Chirality : 0.040 0.121 486 Planarity : 0.004 0.065 551 Dihedral : 6.043 34.846 455 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.39 % Allowed : 28.36 % Favored : 67.25 % 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: -1.10 (0.46), residues: 376 helix: 0.30 (0.34), residues: 253 sheet: -3.16 (1.83), residues: 12 loop : -2.82 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.002 0.000 HIS R 363 PHE 0.009 0.001 PHE R 315 TYR 0.025 0.002 TYR R 235 ARG 0.003 0.000 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 162) hydrogen bonds : angle 3.67938 ( 477) SS BOND : bond 0.00521 ( 4) SS BOND : angle 1.15028 ( 8) covalent geometry : bond 0.00267 ( 3309) covalent geometry : angle 0.64431 ( 4511) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.373 Fit side-chains REVERT: R 34 GLU cc_start: 0.9035 (mp0) cc_final: 0.8774 (mp0) REVERT: R 64 ARG cc_start: 0.6794 (ptp-170) cc_final: 0.6216 (ptp-170) REVERT: R 68 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8660 (mm-30) REVERT: R 269 TYR cc_start: 0.8124 (m-10) cc_final: 0.7545 (m-80) REVERT: R 394 GLN cc_start: 0.9075 (pp30) cc_final: 0.8775 (pp30) REVERT: R 404 PHE cc_start: 0.6260 (OUTLIER) cc_final: 0.5645 (m-80) outliers start: 15 outliers final: 11 residues processed: 79 average time/residue: 0.1105 time to fit residues: 11.2927 Evaluate side-chains 75 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 6 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.128412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.113176 restraints weight = 8506.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.116290 restraints weight = 4313.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.118324 restraints weight = 2594.851| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3313 Z= 0.111 Angle : 0.649 9.787 4519 Z= 0.309 Chirality : 0.039 0.115 486 Planarity : 0.004 0.066 551 Dihedral : 5.632 30.511 455 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.51 % Allowed : 28.36 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.46), residues: 376 helix: 0.34 (0.34), residues: 254 sheet: -2.79 (1.91), residues: 12 loop : -2.72 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 243 HIS 0.001 0.000 HIS R 212 PHE 0.010 0.001 PHE R 280 TYR 0.010 0.001 TYR R 42 ARG 0.003 0.000 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 162) hydrogen bonds : angle 3.47010 ( 477) SS BOND : bond 0.00490 ( 4) SS BOND : angle 1.03908 ( 8) covalent geometry : bond 0.00238 ( 3309) covalent geometry : angle 0.64785 ( 4511) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 34 GLU cc_start: 0.9063 (mp0) cc_final: 0.8746 (mp0) REVERT: R 269 TYR cc_start: 0.8072 (m-10) cc_final: 0.7527 (m-80) REVERT: R 404 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.5717 (m-80) outliers start: 12 outliers final: 9 residues processed: 79 average time/residue: 0.1106 time to fit residues: 11.3660 Evaluate side-chains 77 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.123163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.108761 restraints weight = 8789.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.111791 restraints weight = 4337.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.113742 restraints weight = 2557.052| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3313 Z= 0.183 Angle : 0.701 7.233 4519 Z= 0.348 Chirality : 0.043 0.144 486 Planarity : 0.005 0.070 551 Dihedral : 6.025 35.260 455 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.68 % Allowed : 29.24 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.46), residues: 376 helix: 0.38 (0.34), residues: 248 sheet: -2.92 (1.83), residues: 12 loop : -2.63 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 243 HIS 0.004 0.001 HIS R 363 PHE 0.012 0.002 PHE R 367 TYR 0.025 0.002 TYR R 235 ARG 0.003 0.000 ARG R 421 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 162) hydrogen bonds : angle 3.90604 ( 477) SS BOND : bond 0.00543 ( 4) SS BOND : angle 1.01318 ( 8) covalent geometry : bond 0.00416 ( 3309) covalent geometry : angle 0.70007 ( 4511) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: R 34 GLU cc_start: 0.9080 (mp0) cc_final: 0.8710 (mp0) REVERT: R 269 TYR cc_start: 0.8181 (m-10) cc_final: 0.7692 (m-80) REVERT: R 404 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.5716 (m-80) outliers start: 16 outliers final: 14 residues processed: 72 average time/residue: 0.1236 time to fit residues: 11.3923 Evaluate side-chains 78 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.125694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.110843 restraints weight = 8896.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.113890 restraints weight = 4504.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.115845 restraints weight = 2700.432| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3313 Z= 0.127 Angle : 0.660 7.046 4519 Z= 0.322 Chirality : 0.041 0.139 486 Planarity : 0.005 0.071 551 Dihedral : 5.748 28.657 455 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.80 % Allowed : 30.41 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.46), residues: 376 helix: 0.47 (0.34), residues: 248 sheet: -2.67 (1.83), residues: 12 loop : -2.60 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 243 HIS 0.002 0.001 HIS R 363 PHE 0.010 0.001 PHE R 367 TYR 0.009 0.001 TYR R 402 ARG 0.002 0.000 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 162) hydrogen bonds : angle 3.65469 ( 477) SS BOND : bond 0.00484 ( 4) SS BOND : angle 1.02500 ( 8) covalent geometry : bond 0.00286 ( 3309) covalent geometry : angle 0.65880 ( 4511) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: R 34 GLU cc_start: 0.9032 (mp0) cc_final: 0.8693 (mp0) REVERT: R 269 TYR cc_start: 0.8175 (m-10) cc_final: 0.7634 (m-80) REVERT: R 404 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5666 (m-80) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.1175 time to fit residues: 10.3390 Evaluate side-chains 72 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 17 optimal weight: 0.0970 chunk 13 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.0970 overall best weight: 2.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.125337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.110570 restraints weight = 8599.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.113666 restraints weight = 4321.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.115620 restraints weight = 2578.631| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3313 Z= 0.128 Angle : 0.672 7.826 4519 Z= 0.325 Chirality : 0.041 0.132 486 Planarity : 0.004 0.042 551 Dihedral : 5.592 27.507 455 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.80 % Allowed : 31.29 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.46), residues: 376 helix: 0.50 (0.34), residues: 248 sheet: -2.53 (1.83), residues: 12 loop : -2.58 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 243 HIS 0.002 0.000 HIS R 363 PHE 0.010 0.001 PHE R 367 TYR 0.016 0.001 TYR R 148 ARG 0.002 0.000 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 162) hydrogen bonds : angle 3.64899 ( 477) SS BOND : bond 0.00481 ( 4) SS BOND : angle 1.00934 ( 8) covalent geometry : bond 0.00288 ( 3309) covalent geometry : angle 0.67134 ( 4511) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: R 34 GLU cc_start: 0.9007 (mp0) cc_final: 0.8711 (mp0) REVERT: R 269 TYR cc_start: 0.8152 (m-10) cc_final: 0.7574 (m-80) REVERT: R 404 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.5715 (m-80) outliers start: 13 outliers final: 11 residues processed: 66 average time/residue: 0.1239 time to fit residues: 10.4036 Evaluate side-chains 72 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 17 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.125455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.110638 restraints weight = 8842.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.113695 restraints weight = 4482.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.115646 restraints weight = 2679.848| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3313 Z= 0.136 Angle : 0.664 7.123 4519 Z= 0.325 Chirality : 0.041 0.129 486 Planarity : 0.005 0.077 551 Dihedral : 5.582 27.468 455 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.39 % Allowed : 30.41 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.46), residues: 376 helix: 0.50 (0.34), residues: 248 sheet: -2.56 (1.81), residues: 12 loop : -2.58 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 243 HIS 0.002 0.001 HIS R 363 PHE 0.009 0.001 PHE R 367 TYR 0.011 0.001 TYR R 235 ARG 0.002 0.000 ARG R 421 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 162) hydrogen bonds : angle 3.67683 ( 477) SS BOND : bond 0.00489 ( 4) SS BOND : angle 1.01891 ( 8) covalent geometry : bond 0.00310 ( 3309) covalent geometry : angle 0.66299 ( 4511) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1272.66 seconds wall clock time: 22 minutes 43.61 seconds (1363.61 seconds total)