Starting phenix.real_space_refine on Tue Aug 4 12:46:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k88_62164/08_2026/9k88_62164.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k88_62164/08_2026/9k88_62164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k88_62164/08_2026/9k88_62164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k88_62164/08_2026/9k88_62164.map" model { file = "/net/cci-nas-00/data/ceres_data/9k88_62164/08_2026/9k88_62164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k88_62164/08_2026/9k88_62164.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 24 5.16 5 C 1987 2.51 5 N 455 2.21 5 O 497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2963 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2944 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'NOS%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 0.75, per 1000 atoms: 0.25 Number of scatterers: 2963 At special positions: 0 Unit cell: (68.2, 62.7, 73.7, 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 24 16.00 O 497 8.00 N 455 7.00 C 1987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 375 " 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: 0.17 Conformation dependent library (CDL) restraints added in 66.0 milliseconds 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 83.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 31 through 59 removed outlier: 4.703A pdb=" N VAL A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TRP A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 82 removed outlier: 3.814A pdb=" N ASN A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 89 through 111 Processing helix chain 'A' and resid 112 through 144 removed outlier: 4.649A pdb=" N CYS A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 172 removed outlier: 4.001A pdb=" N GLY A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 210 removed outlier: 3.730A pdb=" N LEU A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 210 " --> pdb=" O CYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 removed outlier: 3.515A pdb=" N LEU A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 257 removed outlier: 3.580A pdb=" N VAL A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 270 Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.695A pdb=" N THR A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.619A pdb=" N LYS A 303 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASN A 304 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 305 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR A 306 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 317 through 320 Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.739A pdb=" N TRP A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 360 removed outlier: 3.502A pdb=" N GLN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 350 " --> pdb=" O CYS A 346 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 374 through 399 removed outlier: 3.842A pdb=" N ILE A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 399 " --> pdb=" O CYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 406 201 hydrogen bonds defined for protein. 585 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: 0.37 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 647 1.33 - 1.45: 665 1.45 - 1.57: 1695 1.57 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 3042 Sorted by residual: bond pdb=" CA ILE A 323 " pdb=" CB ILE A 323 " ideal model delta sigma weight residual 1.539 1.545 -0.006 5.40e-03 3.43e+04 1.35e+00 bond pdb=" CD GLU A 379 " pdb=" OE2 GLU A 379 " ideal model delta sigma weight residual 1.249 1.229 0.020 1.90e-02 2.77e+03 1.09e+00 bond pdb=" N PRO A 293 " pdb=" CA PRO A 293 " ideal model delta sigma weight residual 1.465 1.484 -0.019 2.03e-02 2.43e+03 8.70e-01 bond pdb=" CA VAL A 360 " pdb=" CB VAL A 360 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.11e-01 bond pdb=" CA SER A 143 " pdb=" C SER A 143 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.34e-02 5.57e+03 5.81e-01 ... (remaining 3037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 4018 1.39 - 2.79: 87 2.79 - 4.18: 16 4.18 - 5.57: 10 5.57 - 6.97: 2 Bond angle restraints: 4133 Sorted by residual: angle pdb=" N PRO A 293 " pdb=" CA PRO A 293 " pdb=" C PRO A 293 " ideal model delta sigma weight residual 110.70 113.74 -3.04 1.22e+00 6.72e-01 6.21e+00 angle pdb=" C ASP A 147 " pdb=" N ASN A 148 " pdb=" CA ASN A 148 " ideal model delta sigma weight residual 121.31 124.33 -3.02 1.49e+00 4.50e-01 4.11e+00 angle pdb=" N TYR A 292 " pdb=" CA TYR A 292 " pdb=" C TYR A 292 " ideal model delta sigma weight residual 109.81 114.27 -4.46 2.21e+00 2.05e-01 4.07e+00 angle pdb=" CA LEU A 121 " pdb=" CB LEU A 121 " pdb=" CG LEU A 121 " ideal model delta sigma weight residual 116.30 123.27 -6.97 3.50e+00 8.16e-02 3.96e+00 angle pdb=" N PHE A 257 " pdb=" CA PHE A 257 " pdb=" C PHE A 257 " ideal model delta sigma weight residual 112.75 115.41 -2.66 1.36e+00 5.41e-01 3.82e+00 ... (remaining 4128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 1607 16.80 - 33.59: 118 33.59 - 50.39: 36 50.39 - 67.19: 6 67.19 - 83.98: 1 Dihedral angle restraints: 1768 sinusoidal: 687 harmonic: 1081 Sorted by residual: dihedral pdb=" CA ASP A 238 " pdb=" C ASP A 238 " pdb=" N SER A 239 " pdb=" CA SER A 239 " ideal model delta harmonic sigma weight residual -180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LEU A 256 " pdb=" C LEU A 256 " pdb=" N PHE A 257 " pdb=" CA PHE A 257 " ideal model delta harmonic sigma weight residual -180.00 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA GLY A 142 " pdb=" C GLY A 142 " pdb=" N SER A 143 " pdb=" CA SER A 143 " ideal model delta harmonic sigma weight residual -180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 1765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 245 0.025 - 0.051: 140 0.051 - 0.076: 66 0.076 - 0.101: 28 0.101 - 0.127: 11 Chirality restraints: 490 Sorted by residual: chirality pdb=" CA PRO A 335 " pdb=" N PRO A 335 " pdb=" C PRO A 335 " pdb=" CB PRO A 335 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA PHE A 305 " pdb=" N PHE A 305 " pdb=" C PHE A 305 " pdb=" CB PHE A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA LYS A 373 " pdb=" N LYS A 373 " pdb=" C LYS A 373 " pdb=" CB LYS A 373 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.35e-01 ... (remaining 487 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 293 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 294 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 294 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 294 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 374 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C LYS A 374 " -0.023 2.00e-02 2.50e+03 pdb=" O LYS A 374 " 0.009 2.00e-02 2.50e+03 pdb=" N CYS A 375 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 292 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 293 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " 0.017 5.00e-02 4.00e+02 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 20 2.65 - 3.21: 2856 3.21 - 3.78: 4503 3.78 - 4.34: 5816 4.34 - 4.90: 9735 Nonbonded interactions: 22930 Sorted by model distance: nonbonded pdb=" OH TYR A 65 " pdb=" OD2 ASP A 117 " model vdw 2.090 3.040 nonbonded pdb=" OE1 GLN A 255 " pdb=" OH TYR A 403 " model vdw 2.199 3.040 nonbonded pdb=" NE2 HIS A 269 " pdb=" O ASN A 329 " model vdw 2.277 3.120 nonbonded pdb=" OD1 ASN A 329 " pdb=" NE2 GLN A 342 " model vdw 2.292 3.120 nonbonded pdb=" OG SER A 308 " pdb=" N LEU A 309 " model vdw 2.409 3.120 ... (remaining 22925 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: 1.540 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.670 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 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 0.022 3043 Z= 0.153 Angle : 0.581 6.967 4135 Z= 0.315 Chirality : 0.042 0.127 490 Planarity : 0.004 0.043 495 Dihedral : 13.475 83.981 1065 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.13 % Allowed : 10.67 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.45), residues: 367 helix: 1.96 (0.31), residues: 270 sheet: None (None), residues: 0 loop : -0.29 (0.69), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 319 TYR 0.017 0.001 TYR A 240 PHE 0.014 0.001 PHE A 63 TRP 0.004 0.001 TRP A 251 HIS 0.007 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 ( 3042) covalent geometry : angle 0.58075 / 0.32 ( 4133) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 0.57813 / 0.30 ( 2) hydrogen bonds : bond 0.14413 / 9.90 ( 201) hydrogen bonds : angle 4.60127 / 3.58 ( 585) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.063 Fit side-chains REVERT: A 49 SER cc_start: 0.8055 (t) cc_final: 0.7820 (p) REVERT: A 168 ASN cc_start: 0.6408 (m-40) cc_final: 0.6156 (t0) REVERT: A 264 LYS cc_start: 0.7374 (mttm) cc_final: 0.6867 (tmtt) REVERT: A 313 LEU cc_start: 0.6346 (mt) cc_final: 0.6039 (mt) REVERT: A 401 TYR cc_start: 0.6530 (m-80) cc_final: 0.6121 (m-80) outliers start: 7 outliers final: 1 residues processed: 78 average time/residue: 0.0321 time to fit residues: 3.2127 Evaluate side-chains 62 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.0000 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.0870 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 overall best weight: 0.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.198598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.182140 restraints weight = 5767.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.185251 restraints weight = 3906.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.187544 restraints weight = 2891.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.189045 restraints weight = 2280.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.190382 restraints weight = 1901.045| |-----------------------------------------------------------------------------| r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5420 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 3043 Z= 0.161 Angle : 0.632 8.235 4135 Z= 0.334 Chirality : 0.042 0.130 490 Planarity : 0.004 0.040 495 Dihedral : 6.832 57.979 407 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.18 % Allowed : 14.33 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.44), residues: 367 helix: 1.89 (0.31), residues: 277 sheet: None (None), residues: 0 loop : -1.15 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.011 0.001 TYR A 240 PHE 0.011 0.001 PHE A 63 TRP 0.017 0.001 TRP A 265 HIS 0.008 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 ( 3042) covalent geometry : angle 0.62077 / 0.33 ( 4133) SS BOND : bond 0.02601 / 1.37 ( 1) SS BOND : angle 5.53475 / 2.92 ( 2) hydrogen bonds : bond 0.05885 / 3.87 ( 201) hydrogen bonds : angle 3.88588 / 2.94 ( 585) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 145 MET cc_start: 0.5906 (tpp) cc_final: 0.5396 (tpp) REVERT: A 168 ASN cc_start: 0.6498 (m-40) cc_final: 0.6120 (t0) REVERT: A 269 HIS cc_start: 0.6796 (m-70) cc_final: 0.6499 (m-70) REVERT: A 279 ILE cc_start: 0.7603 (mt) cc_final: 0.7330 (mm) REVERT: A 401 TYR cc_start: 0.6140 (m-80) cc_final: 0.5834 (m-80) outliers start: 17 outliers final: 10 residues processed: 68 average time/residue: 0.0403 time to fit residues: 3.6033 Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 376 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 11 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 HIS A 298 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.195502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.177990 restraints weight = 5758.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.181415 restraints weight = 3875.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.183824 restraints weight = 2847.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.185578 restraints weight = 2231.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.187023 restraints weight = 1835.633| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3043 Z= 0.161 Angle : 0.635 11.148 4135 Z= 0.333 Chirality : 0.044 0.140 490 Planarity : 0.004 0.042 495 Dihedral : 6.778 56.126 407 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.57 % Allowed : 15.85 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.44), residues: 367 helix: 1.70 (0.30), residues: 277 sheet: None (None), residues: 0 loop : -1.59 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 319 TYR 0.010 0.001 TYR A 181 PHE 0.015 0.002 PHE A 63 TRP 0.014 0.002 TRP A 53 HIS 0.007 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 ( 3042) covalent geometry : angle 0.63151 / 0.33 ( 4133) SS BOND : bond 0.01378 / 0.73 ( 1) SS BOND : angle 3.13931 / 1.65 ( 2) hydrogen bonds : bond 0.06044 / 3.93 ( 201) hydrogen bonds : angle 3.95387 / 2.96 ( 585) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.060 Fit side-chains REVERT: A 61 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7157 (mm) REVERT: A 145 MET cc_start: 0.6239 (tpp) cc_final: 0.5871 (tpp) REVERT: A 168 ASN cc_start: 0.6913 (m-40) cc_final: 0.6470 (t0) REVERT: A 187 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7838 (mtmm) REVERT: A 269 HIS cc_start: 0.7150 (m-70) cc_final: 0.6898 (m-70) REVERT: A 401 TYR cc_start: 0.6287 (m-80) cc_final: 0.5826 (m-80) outliers start: 15 outliers final: 8 residues processed: 66 average time/residue: 0.0346 time to fit residues: 3.0273 Evaluate side-chains 66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 393 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 0.0170 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.194149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.176602 restraints weight = 5767.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.179987 restraints weight = 3872.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.182464 restraints weight = 2858.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.184268 restraints weight = 2237.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.185419 restraints weight = 1815.665| |-----------------------------------------------------------------------------| r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3043 Z= 0.154 Angle : 0.659 10.760 4135 Z= 0.331 Chirality : 0.043 0.154 490 Planarity : 0.004 0.041 495 Dihedral : 6.526 53.169 407 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.88 % Allowed : 18.60 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.45), residues: 367 helix: 1.76 (0.31), residues: 277 sheet: None (None), residues: 0 loop : -1.46 (0.71), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.009 0.001 TYR A 240 PHE 0.013 0.001 PHE A 104 TRP 0.020 0.002 TRP A 398 HIS 0.006 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 3042) covalent geometry : angle 0.65770 / 0.33 ( 4133) SS BOND : bond 0.00998 / 0.53 ( 1) SS BOND : angle 2.27527 / 1.20 ( 2) hydrogen bonds : bond 0.05847 / 3.82 ( 201) hydrogen bonds : angle 3.91974 / 2.92 ( 585) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.099 Fit side-chains REVERT: A 61 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7238 (mm) REVERT: A 97 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6668 (mt) REVERT: A 145 MET cc_start: 0.6367 (tpp) cc_final: 0.6166 (tpp) REVERT: A 168 ASN cc_start: 0.7113 (m-40) cc_final: 0.6816 (t0) REVERT: A 187 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7775 (mtmm) REVERT: A 269 HIS cc_start: 0.7391 (m-70) cc_final: 0.7169 (m-70) outliers start: 16 outliers final: 9 residues processed: 67 average time/residue: 0.0268 time to fit residues: 2.4575 Evaluate side-chains 70 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 393 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.191325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.174078 restraints weight = 5692.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.177263 restraints weight = 3879.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.179709 restraints weight = 2900.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.181413 restraints weight = 2284.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.182673 restraints weight = 1875.359| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5622 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3043 Z= 0.188 Angle : 0.659 9.024 4135 Z= 0.351 Chirality : 0.045 0.136 490 Planarity : 0.005 0.047 495 Dihedral : 6.759 52.180 407 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.49 % Allowed : 18.29 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.44), residues: 367 helix: 1.70 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -1.23 (0.67), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.011 0.001 TYR A 181 PHE 0.019 0.002 PHE A 305 TRP 0.022 0.003 TRP A 398 HIS 0.006 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 ( 3042) covalent geometry : angle 0.65816 / 0.35 ( 4133) SS BOND : bond 0.00931 / 0.49 ( 1) SS BOND : angle 1.84857 / 0.97 ( 2) hydrogen bonds : bond 0.06600 / 4.29 ( 201) hydrogen bonds : angle 4.09486 / 3.04 ( 585) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.062 Fit side-chains REVERT: A 61 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7481 (mm) REVERT: A 89 MET cc_start: 0.4321 (mpp) cc_final: 0.3951 (pmm) REVERT: A 168 ASN cc_start: 0.7275 (m-40) cc_final: 0.7018 (t0) REVERT: A 187 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7832 (mtmm) REVERT: A 269 HIS cc_start: 0.7479 (m-70) cc_final: 0.7266 (m-70) outliers start: 18 outliers final: 14 residues processed: 63 average time/residue: 0.0316 time to fit residues: 2.6732 Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 393 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 0.6980 chunk 14 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.102 > 50:) chunk 28 optimal weight: 0.0030 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 0.0020 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 11 optimal weight: 7.9990 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.193803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.176500 restraints weight = 5574.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.179926 restraints weight = 3744.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.182361 restraints weight = 2746.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.184092 restraints weight = 2147.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.185336 restraints weight = 1755.258| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5549 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3043 Z= 0.139 Angle : 0.625 9.621 4135 Z= 0.318 Chirality : 0.041 0.132 490 Planarity : 0.004 0.042 495 Dihedral : 6.556 51.243 407 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.35 % Allowed : 22.87 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.45), residues: 367 helix: 1.92 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -1.16 (0.67), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.006 0.001 TYR A 240 PHE 0.015 0.001 PHE A 247 TRP 0.009 0.001 TRP A 398 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 3042) covalent geometry : angle 0.62416 / 0.32 ( 4133) SS BOND : bond 0.00598 / 0.31 ( 1) SS BOND : angle 1.23520 / 0.65 ( 2) hydrogen bonds : bond 0.05483 / 3.58 ( 201) hydrogen bonds : angle 3.86915 / 2.86 ( 585) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.105 Fit side-chains REVERT: A 61 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7307 (mm) REVERT: A 168 ASN cc_start: 0.7179 (m-40) cc_final: 0.6913 (t0) REVERT: A 187 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7823 (mtmm) REVERT: A 239 SER cc_start: 0.6592 (p) cc_final: 0.6341 (p) outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.0401 time to fit residues: 3.3394 Evaluate side-chains 62 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 393 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.193483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.175490 restraints weight = 5575.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.179054 restraints weight = 3725.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.181530 restraints weight = 2724.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.183121 restraints weight = 2121.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.184479 restraints weight = 1760.679| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3043 Z= 0.139 Angle : 0.626 12.122 4135 Z= 0.317 Chirality : 0.042 0.189 490 Planarity : 0.004 0.042 495 Dihedral : 6.396 50.811 407 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.27 % Allowed : 23.48 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.45), residues: 367 helix: 2.01 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -1.15 (0.67), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.006 0.001 TYR A 240 PHE 0.014 0.001 PHE A 247 TRP 0.007 0.001 TRP A 398 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 3042) covalent geometry : angle 0.62592 / 0.32 ( 4133) SS BOND : bond 0.00622 / 0.33 ( 1) SS BOND : angle 1.29202 / 0.68 ( 2) hydrogen bonds : bond 0.05315 / 3.51 ( 201) hydrogen bonds : angle 3.86257 / 2.87 ( 585) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.064 Fit side-chains REVERT: A 61 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7317 (mm) REVERT: A 73 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6723 (tp) REVERT: A 167 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6480 (tt) REVERT: A 168 ASN cc_start: 0.7138 (m-40) cc_final: 0.6920 (t0) REVERT: A 187 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7868 (mtmm) REVERT: A 269 HIS cc_start: 0.7368 (m-70) cc_final: 0.7127 (m-70) REVERT: A 288 PHE cc_start: 0.5925 (t80) cc_final: 0.5603 (t80) outliers start: 14 outliers final: 10 residues processed: 59 average time/residue: 0.0260 time to fit residues: 2.1106 Evaluate side-chains 63 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 376 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 HIS A 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.187033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.169764 restraints weight = 5469.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.173079 restraints weight = 3610.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.175550 restraints weight = 2636.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.177238 restraints weight = 2045.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.178461 restraints weight = 1663.185| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5683 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3043 Z= 0.228 Angle : 0.720 8.814 4135 Z= 0.386 Chirality : 0.047 0.140 490 Planarity : 0.005 0.047 495 Dihedral : 6.971 50.539 407 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.96 % Allowed : 24.70 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.44), residues: 367 helix: 1.36 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -1.43 (0.64), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 319 TYR 0.010 0.001 TYR A 181 PHE 0.018 0.002 PHE A 236 TRP 0.024 0.004 TRP A 398 HIS 0.007 0.002 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.23 ( 3042) covalent geometry : angle 0.71996 / 0.39 ( 4133) SS BOND : bond 0.00884 / 0.47 ( 1) SS BOND : angle 1.27633 / 0.68 ( 2) hydrogen bonds : bond 0.07313 / 4.75 ( 201) hydrogen bonds : angle 4.32595 / 3.22 ( 585) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.073 Fit side-chains REVERT: A 61 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7693 (mm) REVERT: A 167 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.6940 (tt) REVERT: A 168 ASN cc_start: 0.7367 (m-40) cc_final: 0.7133 (t0) REVERT: A 187 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7919 (mtmm) REVERT: A 269 HIS cc_start: 0.7479 (m-70) cc_final: 0.7259 (m-70) REVERT: A 288 PHE cc_start: 0.6154 (t80) cc_final: 0.5840 (t80) outliers start: 13 outliers final: 9 residues processed: 61 average time/residue: 0.0339 time to fit residues: 2.8753 Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 346 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.0000 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.189494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.173192 restraints weight = 5442.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.176327 restraints weight = 3591.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.178642 restraints weight = 2630.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.180230 restraints weight = 2039.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.181304 restraints weight = 1658.817| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5630 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3043 Z= 0.176 Angle : 0.667 8.839 4135 Z= 0.352 Chirality : 0.044 0.150 490 Planarity : 0.004 0.045 495 Dihedral : 6.920 49.659 407 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.35 % Allowed : 24.70 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.45), residues: 367 helix: 1.53 (0.32), residues: 268 sheet: None (None), residues: 0 loop : -1.50 (0.64), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.007 0.001 TYR A 181 PHE 0.028 0.002 PHE A 305 TRP 0.013 0.002 TRP A 398 HIS 0.008 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 ( 3042) covalent geometry : angle 0.66622 / 0.35 ( 4133) SS BOND : bond 0.00763 / 0.40 ( 1) SS BOND : angle 1.20364 / 0.64 ( 2) hydrogen bonds : bond 0.06467 / 4.20 ( 201) hydrogen bonds : angle 4.19022 / 3.12 ( 585) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.112 Fit side-chains REVERT: A 61 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7520 (mm) REVERT: A 167 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.6762 (tt) REVERT: A 168 ASN cc_start: 0.7304 (m-40) cc_final: 0.7095 (t0) REVERT: A 187 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7884 (mtmm) REVERT: A 288 PHE cc_start: 0.6226 (t80) cc_final: 0.5854 (t80) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.0391 time to fit residues: 3.2019 Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 346 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 4 optimal weight: 0.1980 chunk 26 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.0570 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.191898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.175684 restraints weight = 5410.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.178927 restraints weight = 3616.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.181254 restraints weight = 2657.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.182790 restraints weight = 2065.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.183542 restraints weight = 1689.621| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5579 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3043 Z= 0.142 Angle : 0.644 8.567 4135 Z= 0.329 Chirality : 0.042 0.127 490 Planarity : 0.004 0.043 495 Dihedral : 6.575 50.027 407 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.35 % Allowed : 25.61 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.45), residues: 367 helix: 1.80 (0.32), residues: 268 sheet: None (None), residues: 0 loop : -1.47 (0.64), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.005 0.001 TYR A 181 PHE 0.015 0.001 PHE A 247 TRP 0.011 0.001 TRP A 398 HIS 0.008 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 3042) covalent geometry : angle 0.64412 / 0.33 ( 4133) SS BOND : bond 0.00554 / 0.29 ( 1) SS BOND : angle 1.13819 / 0.60 ( 2) hydrogen bonds : bond 0.05453 / 3.59 ( 201) hydrogen bonds : angle 3.99032 / 2.94 ( 585) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.063 Fit side-chains REVERT: A 61 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7404 (mm) REVERT: A 167 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7087 (tp) REVERT: A 187 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7857 (mtmm) REVERT: A 288 PHE cc_start: 0.6167 (t80) cc_final: 0.5837 (t80) outliers start: 11 outliers final: 8 residues processed: 60 average time/residue: 0.0349 time to fit residues: 2.8793 Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 346 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.188798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.172407 restraints weight = 5442.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.175662 restraints weight = 3621.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.178046 restraints weight = 2641.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.179641 restraints weight = 2030.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.180812 restraints weight = 1651.157| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5625 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3043 Z= 0.178 Angle : 0.689 8.106 4135 Z= 0.361 Chirality : 0.044 0.130 490 Planarity : 0.004 0.043 495 Dihedral : 6.740 49.660 407 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.66 % Allowed : 24.70 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.45), residues: 367 helix: 1.64 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -1.51 (0.64), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.008 0.001 TYR A 232 PHE 0.015 0.002 PHE A 247 TRP 0.013 0.002 TRP A 398 HIS 0.009 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 ( 3042) covalent geometry : angle 0.68638 / 0.36 ( 4133) SS BOND : bond 0.01354 / 0.71 ( 1) SS BOND : angle 2.79973 / 1.52 ( 2) hydrogen bonds : bond 0.06197 / 4.06 ( 201) hydrogen bonds : angle 4.12636 / 3.04 ( 585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 646.91 seconds wall clock time: 11 minutes 49.28 seconds (709.28 seconds total)