Starting phenix.real_space_refine on Wed Jun 3 10:04:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k88_62164/06_2026/9k88_62164.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k88_62164/06_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_62164/06_2026/9k88_62164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k88_62164/06_2026/9k88_62164.map" model { file = "/net/cci-nas-00/data/ceres_data/9k88_62164/06_2026/9k88_62164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k88_62164/06_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-dev-6079/lib/python3.9/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: 0.82, per 1000 atoms: 0.28 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: 0.29 Conformation dependent library (CDL) restraints added in 122.6 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: 0.09 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: 0.48 Time building geometry restraints manager: 0.38 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=" C3' NOS A 501 " pdb=" O3' NOS A 501 " ideal model delta sigma weight residual 1.402 1.427 -0.025 2.00e-02 2.50e+03 1.56e+00 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=" C1' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.397 1.420 -0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" C2' NOS A 501 " pdb=" O2' NOS A 501 " ideal model delta sigma weight residual 1.390 1.412 -0.022 2.00e-02 2.50e+03 1.18e+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 ... (remaining 3037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 4009 1.39 - 2.79: 94 2.79 - 4.18: 18 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: 242 0.025 - 0.051: 142 0.051 - 0.076: 66 0.076 - 0.101: 29 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.990 Find NCS groups from input model: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5337 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 0.025 3043 Z= 0.160 Angle : 0.591 6.967 4135 Z= 0.317 Chirality : 0.042 0.127 490 Planarity : 0.004 0.043 495 Dihedral : 13.461 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 0.00300 / 0.16 ( 3042) covalent geometry : angle 0.59052 / 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 : 0.108 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: 0.0502 time to fit residues: 4.9579 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 : 0.074 ------------------------------------------------------------------------------- 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: 0.7980 chunk 16 optimal weight: 0.6980 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: 0.6980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 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 = 0.4497 r_free = 0.4497 target = 0.198520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.181178 restraints weight = 5863.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.184438 restraints weight = 3963.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.186858 restraints weight = 2940.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.188582 restraints weight = 2304.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.189976 restraints weight = 1896.090| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5455 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 3043 Z= 0.160 Angle : 0.635 7.899 4135 Z= 0.336 Chirality : 0.042 0.131 490 Planarity : 0.004 0.041 495 Dihedral : 6.668 57.727 407 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.49 % Allowed : 13.41 % Favored : 81.10 % 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: 1.66 (0.44), residues: 367 helix: 1.83 (0.30), residues: 277 sheet: None (None), residues: 0 loop : -1.23 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.011 0.001 TYR A 240 PHE 0.013 0.001 PHE A 63 TRP 0.016 0.002 TRP A 265 HIS 0.008 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 ( 3042) covalent geometry : angle 0.62635 / 0.33 ( 4133) SS BOND : bond 0.01955 / 1.03 ( 1) SS BOND : angle 4.76958 / 2.52 ( 2) hydrogen bonds : bond 0.05908 / 3.87 ( 201) hydrogen bonds : angle 3.93165 / 2.97 ( 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 75 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.105 Fit side-chains REVERT: A 145 MET cc_start: 0.5984 (tpp) cc_final: 0.5512 (tpp) REVERT: A 168 ASN cc_start: 0.6657 (m-40) cc_final: 0.6208 (t0) REVERT: A 187 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7773 (mtmm) REVERT: A 269 HIS cc_start: 0.6881 (m-70) cc_final: 0.6644 (m-70) REVERT: A 279 ILE cc_start: 0.7669 (mt) cc_final: 0.7358 (mm) REVERT: A 401 TYR cc_start: 0.6219 (m-80) cc_final: 0.5765 (m-80) outliers start: 18 outliers final: 10 residues processed: 67 average time/residue: 0.0421 time to fit residues: 3.7222 Evaluate side-chains 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.119 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.188520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.172269 restraints weight = 5707.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.175753 restraints weight = 3791.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.178085 restraints weight = 2760.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.179741 restraints weight = 2134.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.180920 restraints weight = 1733.801| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5631 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3043 Z= 0.209 Angle : 0.706 10.309 4135 Z= 0.377 Chirality : 0.046 0.143 490 Planarity : 0.005 0.051 495 Dihedral : 6.972 55.768 407 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.66 % Allowed : 18.60 % Favored : 77.74 % 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: 1.02 (0.44), residues: 367 helix: 1.41 (0.31), residues: 277 sheet: None (None), residues: 0 loop : -1.62 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 319 TYR 0.014 0.002 TYR A 181 PHE 0.018 0.002 PHE A 63 TRP 0.022 0.003 TRP A 398 HIS 0.007 0.003 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 ( 3042) covalent geometry : angle 0.70139 / 0.38 ( 4133) SS BOND : bond 0.01736 / 0.91 ( 1) SS BOND : angle 3.63223 / 1.91 ( 2) hydrogen bonds : bond 0.07383 / 4.77 ( 201) hydrogen bonds : angle 4.29976 / 3.22 ( 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 70 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.105 Fit side-chains REVERT: A 61 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7490 (mm) REVERT: A 187 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7929 (mtpp) REVERT: A 269 HIS cc_start: 0.7327 (m-70) cc_final: 0.7077 (m-70) REVERT: A 282 MET cc_start: 0.5416 (tpp) cc_final: 0.4635 (tmm) REVERT: A 401 TYR cc_start: 0.6460 (m-80) cc_final: 0.5926 (m-80) outliers start: 12 outliers final: 5 residues processed: 64 average time/residue: 0.0409 time to fit residues: 3.4939 Evaluate side-chains 60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 254 LEU Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 376 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.0270 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 overall best weight: 0.3038 ------------------------------------------------------------------------------- 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 = 0.4432 r_free = 0.4432 target = 0.192692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.175182 restraints weight = 5595.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.178663 restraints weight = 3682.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.181142 restraints weight = 2666.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.182954 restraints weight = 2058.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.184142 restraints weight = 1671.751| |-----------------------------------------------------------------------------| r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5569 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3043 Z= 0.149 Angle : 0.642 11.006 4135 Z= 0.325 Chirality : 0.042 0.152 490 Planarity : 0.004 0.045 495 Dihedral : 6.530 53.006 407 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.57 % Allowed : 18.90 % 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: 1.69 (0.45), residues: 367 helix: 1.91 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -1.11 (0.65), 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 240 PHE 0.015 0.001 PHE A 247 TRP 0.018 0.002 TRP A 398 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 ( 3042) covalent geometry : angle 0.63978 / 0.32 ( 4133) SS BOND : bond 0.00941 / 0.50 ( 1) SS BOND : angle 2.28677 / 1.21 ( 2) hydrogen bonds : bond 0.05876 / 3.85 ( 201) hydrogen bonds : angle 3.92206 / 2.94 ( 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 73 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.066 Fit side-chains REVERT: A 61 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7360 (mm) REVERT: A 104 PHE cc_start: 0.5451 (OUTLIER) cc_final: 0.5241 (m-80) REVERT: A 187 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7810 (mtmm) REVERT: A 269 HIS cc_start: 0.7358 (m-70) cc_final: 0.7115 (m-70) outliers start: 15 outliers final: 9 residues processed: 70 average time/residue: 0.0361 time to fit residues: 3.3942 Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 98 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 298 HIS 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: 0.0070 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.0050 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.4012 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.192222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.174657 restraints weight = 5549.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.178061 restraints weight = 3707.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.180550 restraints weight = 2711.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.182321 restraints weight = 2109.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.183627 restraints weight = 1725.572| |-----------------------------------------------------------------------------| r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.3809 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= 0.162 Angle : 0.636 9.947 4135 Z= 0.333 Chirality : 0.043 0.132 490 Planarity : 0.004 0.048 495 Dihedral : 6.573 52.717 407 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.88 % Allowed : 20.12 % Favored : 75.00 % 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: 1.62 (0.45), residues: 367 helix: 1.88 (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 0.008 0.001 TYR A 181 PHE 0.016 0.001 PHE A 305 TRP 0.008 0.002 TRP A 356 HIS 0.006 0.002 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 ( 3042) covalent geometry : angle 0.63403 / 0.33 ( 4133) SS BOND : bond 0.00895 / 0.47 ( 1) SS BOND : angle 2.07143 / 1.09 ( 2) hydrogen bonds : bond 0.06043 / 3.94 ( 201) hydrogen bonds : angle 3.96166 / 2.96 ( 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 69 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.105 Fit side-chains REVERT: A 61 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7432 (mm) REVERT: A 89 MET cc_start: 0.4340 (mpp) cc_final: 0.3995 (pmm) REVERT: A 104 PHE cc_start: 0.5450 (OUTLIER) cc_final: 0.5196 (m-80) REVERT: A 187 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7813 (mtmm) outliers start: 16 outliers final: 13 residues processed: 62 average time/residue: 0.0374 time to fit residues: 3.1416 Evaluate side-chains 67 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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 98 SER Chi-restraints excluded: chain A residue 104 PHE 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 272 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 298 HIS 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: 0.4980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 chunk 26 optimal weight: 0.0970 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 11 optimal weight: 0.4980 overall best weight: 0.1676 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.195444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.177878 restraints weight = 5598.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.181292 restraints weight = 3752.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.183728 restraints weight = 2754.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.185519 restraints weight = 2159.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.186834 restraints weight = 1773.284| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3043 Z= 0.130 Angle : 0.609 10.485 4135 Z= 0.307 Chirality : 0.041 0.138 490 Planarity : 0.004 0.043 495 Dihedral : 6.266 52.738 407 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.57 % Allowed : 22.56 % Favored : 72.87 % 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: 1.87 (0.45), residues: 367 helix: 2.08 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -1.17 (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 0.016 0.001 TRP A 398 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 ( 3042) covalent geometry : angle 0.60832 / 0.31 ( 4133) SS BOND : bond 0.00510 / 0.27 ( 1) SS BOND : angle 1.46341 / 0.77 ( 2) hydrogen bonds : bond 0.05056 / 3.31 ( 201) hydrogen bonds : angle 3.75032 / 2.79 ( 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 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.102 Fit side-chains REVERT: A 61 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7239 (mm) REVERT: A 73 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6637 (tp) REVERT: A 104 PHE cc_start: 0.5245 (OUTLIER) cc_final: 0.4951 (m-80) REVERT: A 187 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7821 (mtmm) REVERT: A 239 SER cc_start: 0.6544 (p) cc_final: 0.6296 (p) outliers start: 15 outliers final: 10 residues processed: 63 average time/residue: 0.0364 time to fit residues: 3.0986 Evaluate side-chains 66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.062 ------------------------------------------------------------------------------- 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 104 PHE 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 268 SER Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 376 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.192529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.174824 restraints weight = 5556.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.178242 restraints weight = 3721.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.180740 restraints weight = 2721.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.182463 restraints weight = 2127.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.183596 restraints weight = 1738.824| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3043 Z= 0.148 Angle : 0.622 9.308 4135 Z= 0.320 Chirality : 0.042 0.131 490 Planarity : 0.004 0.045 495 Dihedral : 6.298 52.626 407 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.27 % Allowed : 24.39 % 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: 1.79 (0.45), residues: 367 helix: 2.04 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -1.24 (0.67), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.008 0.001 TYR A 240 PHE 0.014 0.001 PHE A 247 TRP 0.009 0.002 TRP A 398 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 ( 3042) covalent geometry : angle 0.62171 / 0.32 ( 4133) SS BOND : bond 0.00683 / 0.36 ( 1) SS BOND : angle 1.40582 / 0.74 ( 2) hydrogen bonds : bond 0.05540 / 3.64 ( 201) hydrogen bonds : angle 3.87852 / 2.88 ( 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 66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.103 Fit side-chains REVERT: A 61 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7437 (mm) REVERT: A 104 PHE cc_start: 0.5294 (OUTLIER) cc_final: 0.4956 (m-80) REVERT: A 167 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.6658 (tt) REVERT: A 187 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7867 (mtmm) outliers start: 14 outliers final: 11 residues processed: 60 average time/residue: 0.0355 time to fit residues: 2.9268 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 : 0.114 ------------------------------------------------------------------------------- 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 104 PHE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 198 CYS 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 346 CYS 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: 0.5980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.0170 chunk 28 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.190982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.173888 restraints weight = 5556.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.177340 restraints weight = 3722.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.179446 restraints weight = 2721.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.181287 restraints weight = 2160.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.182421 restraints weight = 1759.144| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3043 Z= 0.158 Angle : 0.654 11.563 4135 Z= 0.333 Chirality : 0.043 0.161 490 Planarity : 0.004 0.045 495 Dihedral : 6.326 51.916 407 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.57 % Allowed : 24.70 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.59 (0.45), residues: 367 helix: 1.90 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -1.34 (0.65), 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 181 PHE 0.014 0.002 PHE A 247 TRP 0.010 0.002 TRP A 356 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 ( 3042) covalent geometry : angle 0.65361 / 0.33 ( 4133) SS BOND : bond 0.00682 / 0.36 ( 1) SS BOND : angle 1.27655 / 0.68 ( 2) hydrogen bonds : bond 0.05844 / 3.81 ( 201) hydrogen bonds : angle 3.95706 / 2.94 ( 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 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.099 Fit side-chains REVERT: A 61 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7431 (mm) REVERT: A 73 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6607 (tp) REVERT: A 104 PHE cc_start: 0.5306 (OUTLIER) cc_final: 0.4984 (m-80) REVERT: A 167 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.6818 (tt) REVERT: A 187 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7796 (mtmm) outliers start: 15 outliers final: 9 residues processed: 59 average time/residue: 0.0357 time to fit residues: 2.8394 Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 104 PHE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 136 THR 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 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: 0.7980 chunk 24 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 36 optimal weight: 0.0020 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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 = 0.4393 r_free = 0.4393 target = 0.191420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.174269 restraints weight = 5649.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.177610 restraints weight = 3849.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.179970 restraints weight = 2861.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.181610 restraints weight = 2258.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.182776 restraints weight = 1860.535| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5606 moved from start: 0.4723 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= 0.156 Angle : 0.649 8.931 4135 Z= 0.333 Chirality : 0.042 0.134 490 Planarity : 0.004 0.044 495 Dihedral : 6.367 51.486 407 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.27 % Allowed : 26.22 % Favored : 69.51 % 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: 1.52 (0.44), residues: 367 helix: 1.90 (0.31), residues: 262 sheet: None (None), residues: 0 loop : -1.33 (0.63), residues: 105 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 0.014 0.001 PHE A 247 TRP 0.009 0.002 TRP A 356 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 ( 3042) covalent geometry : angle 0.64827 / 0.33 ( 4133) SS BOND : bond 0.00655 / 0.34 ( 1) SS BOND : angle 1.23429 / 0.65 ( 2) hydrogen bonds : bond 0.05827 / 3.80 ( 201) hydrogen bonds : angle 3.99749 / 2.97 ( 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 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.065 Fit side-chains REVERT: A 61 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7505 (mm) REVERT: A 104 PHE cc_start: 0.5283 (OUTLIER) cc_final: 0.4955 (m-80) REVERT: A 165 PHE cc_start: 0.6256 (t80) cc_final: 0.6030 (t80) REVERT: A 167 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.6851 (tt) REVERT: A 187 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7802 (mtmm) outliers start: 14 outliers final: 11 residues processed: 59 average time/residue: 0.0345 time to fit residues: 2.7078 Evaluate side-chains 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.097 ------------------------------------------------------------------------------- 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 104 PHE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 198 CYS 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 346 CYS Chi-restraints excluded: chain A residue 376 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 31 optimal weight: 0.1980 chunk 36 optimal weight: 0.0770 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.191448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.174580 restraints weight = 5445.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.177848 restraints weight = 3678.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.180208 restraints weight = 2711.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.181768 restraints weight = 2122.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.183002 restraints weight = 1754.502| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5588 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3043 Z= 0.148 Angle : 0.640 8.877 4135 Z= 0.329 Chirality : 0.042 0.138 490 Planarity : 0.004 0.043 495 Dihedral : 6.384 51.225 407 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.27 % Allowed : 26.22 % Favored : 69.51 % 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: 1.53 (0.45), residues: 367 helix: 1.93 (0.31), residues: 262 sheet: None (None), residues: 0 loop : -1.41 (0.63), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.007 0.001 TYR A 232 PHE 0.020 0.001 PHE A 305 TRP 0.008 0.002 TRP A 356 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 ( 3042) covalent geometry : angle 0.63981 / 0.33 ( 4133) SS BOND : bond 0.00630 / 0.33 ( 1) SS BOND : angle 1.18936 / 0.63 ( 2) hydrogen bonds : bond 0.05662 / 3.69 ( 201) hydrogen bonds : angle 3.98205 / 2.95 ( 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 69 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.100 Fit side-chains REVERT: A 61 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7418 (mm) REVERT: A 104 PHE cc_start: 0.5172 (OUTLIER) cc_final: 0.4857 (m-80) REVERT: A 165 PHE cc_start: 0.6209 (t80) cc_final: 0.5998 (t80) REVERT: A 167 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.6804 (tt) REVERT: A 187 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7798 (mtmm) outliers start: 14 outliers final: 11 residues processed: 63 average time/residue: 0.0347 time to fit residues: 3.0487 Evaluate side-chains 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.064 ------------------------------------------------------------------------------- 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 104 PHE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 198 CYS 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 346 CYS Chi-restraints excluded: chain A residue 376 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 36 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.0010 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 34 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.3186 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.191933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.175225 restraints weight = 5370.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.178563 restraints weight = 3593.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.180842 restraints weight = 2635.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.182408 restraints weight = 2060.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.183471 restraints weight = 1692.142| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5569 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3043 Z= 0.141 Angle : 0.632 7.559 4135 Z= 0.321 Chirality : 0.042 0.124 490 Planarity : 0.004 0.042 495 Dihedral : 6.191 51.229 407 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.57 % Allowed : 26.22 % Favored : 69.21 % 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: 1.57 (0.45), residues: 367 helix: 1.97 (0.31), residues: 262 sheet: None (None), residues: 0 loop : -1.40 (0.64), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.007 0.001 TYR A 232 PHE 0.015 0.001 PHE A 247 TRP 0.007 0.001 TRP A 251 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 3042) covalent geometry : angle 0.63205 / 0.32 ( 4133) SS BOND : bond 0.00666 / 0.35 ( 1) SS BOND : angle 1.21141 / 0.64 ( 2) hydrogen bonds : bond 0.05303 / 3.47 ( 201) hydrogen bonds : angle 3.95224 / 2.93 ( 585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 662.36 seconds wall clock time: 12 minutes 8.41 seconds (728.41 seconds total)