Starting phenix.real_space_refine on Tue Aug 4 12:40:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtc_36640/08_2026/8jtc_36640.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtc_36640/08_2026/8jtc_36640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jtc_36640/08_2026/8jtc_36640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtc_36640/08_2026/8jtc_36640.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jtc_36640/08_2026/8jtc_36640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtc_36640/08_2026/8jtc_36640.map" } resolution = 3.52 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= 0.068 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 27 5.16 5 C 1963 2.51 5 N 452 2.21 5 O 499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 2941 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 2897 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 23, 'TRANS': 367} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.75, per 1000 atoms: 0.26 Number of scatterers: 2941 At special positions: 0 Unit cell: (56.16, 67.6, 73.84, 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 27 16.00 O 499 8.00 N 452 7.00 C 1963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.28 Conformation dependent library (CDL) restraints added in 113.7 milliseconds 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 706 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 92.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 18 through 54 removed outlier: 4.013A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 122 through 157 removed outlier: 3.887A pdb=" N VAL A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.678A pdb=" N TYR A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 270 removed outlier: 4.555A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 291 through 323 removed outlier: 4.143A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 328 through 333 removed outlier: 4.041A pdb=" N VAL A 332 " --> pdb=" O TRP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.508A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 414 Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 447 removed outlier: 4.556A pdb=" N TYR A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 4.027A pdb=" N ALA A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 469 259 hydrogen bonds defined for protein. 768 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: 0.54 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 441 1.30 - 1.43: 776 1.43 - 1.56: 1753 1.56 - 1.68: 0 1.68 - 1.81: 46 Bond restraints: 3016 Sorted by residual: bond pdb=" C12 YHR A 501 " pdb=" N21 YHR A 501 " ideal model delta sigma weight residual 1.374 1.217 0.157 2.00e-02 2.50e+03 6.16e+01 bond pdb=" C31 YHR A 501 " pdb=" O30 YHR A 501 " ideal model delta sigma weight residual 1.326 1.410 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C17 YHR A 501 " pdb=" O19 YHR A 501 " ideal model delta sigma weight residual 1.325 1.408 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C22 YHR A 501 " pdb=" N21 YHR A 501 " ideal model delta sigma weight residual 1.365 1.283 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C31 YHR A 501 " pdb=" C33 YHR A 501 " ideal model delta sigma weight residual 1.486 1.549 -0.063 2.00e-02 2.50e+03 1.00e+01 ... (remaining 3011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 4020 2.94 - 5.88: 83 5.88 - 8.83: 7 8.83 - 11.77: 2 11.77 - 14.71: 1 Bond angle restraints: 4113 Sorted by residual: angle pdb=" C12 YHR A 501 " pdb=" N21 YHR A 501 " pdb=" C22 YHR A 501 " ideal model delta sigma weight residual 109.26 123.97 -14.71 3.00e+00 1.11e-01 2.40e+01 angle pdb=" N PRO A 450 " pdb=" CA PRO A 450 " pdb=" C PRO A 450 " ideal model delta sigma weight residual 113.47 108.59 4.88 1.43e+00 4.89e-01 1.16e+01 angle pdb=" CA VAL A 241 " pdb=" C VAL A 241 " pdb=" O VAL A 241 " ideal model delta sigma weight residual 121.17 117.69 3.48 1.06e+00 8.90e-01 1.08e+01 angle pdb=" CA ILE A 223 " pdb=" C ILE A 223 " pdb=" O ILE A 223 " ideal model delta sigma weight residual 121.05 117.52 3.53 1.11e+00 8.12e-01 1.01e+01 angle pdb=" N ILE A 395 " pdb=" CA ILE A 395 " pdb=" C ILE A 395 " ideal model delta sigma weight residual 110.62 107.41 3.21 1.02e+00 9.61e-01 9.93e+00 ... (remaining 4108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 1586 17.24 - 34.48: 177 34.48 - 51.72: 34 51.72 - 68.96: 3 68.96 - 86.20: 1 Dihedral angle restraints: 1801 sinusoidal: 693 harmonic: 1108 Sorted by residual: dihedral pdb=" CA GLN A 271 " pdb=" C GLN A 271 " pdb=" N PRO A 272 " pdb=" CA PRO A 272 " ideal model delta harmonic sigma weight residual 180.00 -149.93 -30.07 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA PHE A 348 " pdb=" C PHE A 348 " pdb=" N GLY A 349 " pdb=" CA GLY A 349 " ideal model delta harmonic sigma weight residual 180.00 164.02 15.98 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA SER A 416 " pdb=" C SER A 416 " pdb=" N VAL A 417 " pdb=" CA VAL A 417 " ideal model delta harmonic sigma weight residual 180.00 164.34 15.66 0 5.00e+00 4.00e-02 9.80e+00 ... (remaining 1798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 379 0.054 - 0.107: 91 0.107 - 0.161: 16 0.161 - 0.214: 6 0.214 - 0.268: 1 Chirality restraints: 493 Sorted by residual: chirality pdb=" C13 YHR A 501 " pdb=" C12 YHR A 501 " pdb=" C14 YHR A 501 " pdb=" N8 YHR A 501 " both_signs ideal model delta sigma weight residual False -2.29 -2.56 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA TYR A 243 " pdb=" N TYR A 243 " pdb=" C TYR A 243 " pdb=" CB TYR A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CA LEU A 452 " pdb=" N LEU A 452 " pdb=" C LEU A 452 " pdb=" CB LEU A 452 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 490 not shown) Planarity restraints: 500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO A 236 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 222 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C GLY A 222 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY A 222 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 223 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 432 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C GLY A 432 " -0.028 2.00e-02 2.50e+03 pdb=" O GLY A 432 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 433 " 0.009 2.00e-02 2.50e+03 ... (remaining 497 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 637 2.77 - 3.30: 3048 3.30 - 3.84: 5131 3.84 - 4.37: 5633 4.37 - 4.90: 10005 Nonbonded interactions: 24454 Sorted by model distance: nonbonded pdb=" OG SER A 325 " pdb=" OE1 GLN A 329 " model vdw 2.240 3.040 nonbonded pdb=" OG SER A 200 " pdb=" OH TYR A 422 " model vdw 2.398 3.040 nonbonded pdb=" OH TYR A 408 " pdb=" OG SER A 472 " model vdw 2.476 3.040 nonbonded pdb=" O MET A 402 " pdb=" N MET A 406 " model vdw 2.528 3.120 nonbonded pdb=" O MET A 397 " pdb=" OG SER A 401 " model vdw 2.534 3.040 ... (remaining 24449 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: 1.320 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: 0.010 Set scattering table: 0.010 Process input model: 4.770 Find NCS groups from input model: 0.010 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: 0.000 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.007 0.157 3016 Z= 0.364 Angle : 0.944 14.709 4113 Z= 0.488 Chirality : 0.050 0.268 493 Planarity : 0.006 0.066 500 Dihedral : 14.323 86.204 1095 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.33 % Allowed : 22.37 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.35 % 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: 1.13 (0.43), residues: 387 helix: 1.16 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.21 (0.77), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.016 0.001 TYR A 243 PHE 0.020 0.001 PHE A 348 TRP 0.011 0.002 TRP A 451 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.36 ( 3016) covalent geometry : angle 0.94392 / 0.49 ( 4113) hydrogen bonds : bond 0.12408 / 7.79 ( 259) hydrogen bonds : angle 6.48892 / 4.92 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.114 Fit side-chains REVERT: A 402 MET cc_start: 0.8442 (mmt) cc_final: 0.8241 (mmt) outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.0719 time to fit residues: 5.3795 Evaluate side-chains 58 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 30 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.4459 > 50:) chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114102 restraints weight = 4512.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117444 restraints weight = 2171.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119709 restraints weight = 1290.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121261 restraints weight = 869.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122350 restraints weight = 635.947| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3016 Z= 0.166 Angle : 0.719 9.843 4113 Z= 0.341 Chirality : 0.043 0.196 493 Planarity : 0.006 0.044 500 Dihedral : 5.208 29.698 477 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.63 % Allowed : 20.39 % Favored : 76.97 % 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: 1.81 (0.42), residues: 387 helix: 1.62 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -1.07 (0.81), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.007 0.001 TYR A 211 PHE 0.021 0.001 PHE A 348 TRP 0.010 0.001 TRP A 451 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 3016) covalent geometry : angle 0.71870 / 0.34 ( 4113) hydrogen bonds : bond 0.04311 / 2.84 ( 259) hydrogen bonds : angle 4.75099 / 3.56 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.105 Fit side-chains REVERT: A 402 MET cc_start: 0.8669 (mmt) cc_final: 0.8070 (mmm) outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.0544 time to fit residues: 5.0191 Evaluate side-chains 68 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.126913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.113784 restraints weight = 4569.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117143 restraints weight = 2189.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119362 restraints weight = 1295.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120854 restraints weight = 877.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121903 restraints weight = 649.629| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3016 Z= 0.159 Angle : 0.710 9.871 4113 Z= 0.335 Chirality : 0.042 0.191 493 Planarity : 0.005 0.038 500 Dihedral : 5.063 29.201 477 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.96 % Allowed : 21.05 % Favored : 75.99 % 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: 2.12 (0.43), residues: 387 helix: 1.86 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -1.11 (0.80), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 357 TYR 0.008 0.001 TYR A 211 PHE 0.020 0.001 PHE A 348 TRP 0.005 0.001 TRP A 318 HIS 0.001 0.000 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 3016) covalent geometry : angle 0.70953 / 0.34 ( 4113) hydrogen bonds : bond 0.04173 / 2.75 ( 259) hydrogen bonds : angle 4.53721 / 3.40 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.113 Fit side-chains REVERT: A 326 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.7938 (mtm180) REVERT: A 402 MET cc_start: 0.8593 (mmt) cc_final: 0.8371 (mmm) outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 0.0643 time to fit residues: 5.6322 Evaluate side-chains 68 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 29 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.128411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.115258 restraints weight = 4512.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118609 restraints weight = 2183.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120867 restraints weight = 1300.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122329 restraints weight = 877.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123394 restraints weight = 655.720| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3016 Z= 0.150 Angle : 0.685 9.781 4113 Z= 0.326 Chirality : 0.042 0.185 493 Planarity : 0.005 0.038 500 Dihedral : 4.715 27.062 475 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.29 % Allowed : 23.03 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.16 (0.43), residues: 387 helix: 1.87 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -1.04 (0.81), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.008 0.001 TYR A 211 PHE 0.018 0.001 PHE A 348 TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 3016) covalent geometry : angle 0.68496 / 0.33 ( 4113) hydrogen bonds : bond 0.04040 / 2.66 ( 259) hydrogen bonds : angle 4.45986 / 3.35 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.103 Fit side-chains REVERT: A 142 GLN cc_start: 0.8563 (tt0) cc_final: 0.8352 (tt0) REVERT: A 458 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8333 (mp) REVERT: A 462 LEU cc_start: 0.8877 (mt) cc_final: 0.8630 (mm) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.0711 time to fit residues: 6.1567 Evaluate side-chains 73 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 458 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.128041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114814 restraints weight = 4507.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118169 restraints weight = 2195.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120367 restraints weight = 1315.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121798 restraints weight = 898.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122863 restraints weight = 675.066| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3016 Z= 0.155 Angle : 0.688 9.864 4113 Z= 0.328 Chirality : 0.042 0.175 493 Planarity : 0.005 0.039 500 Dihedral : 4.675 27.450 475 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.28 % Allowed : 23.03 % Favored : 72.70 % 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: 2.19 (0.43), residues: 387 helix: 1.93 (0.28), residues: 327 sheet: None (None), residues: 0 loop : -1.24 (0.82), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.008 0.001 TYR A 211 PHE 0.018 0.001 PHE A 348 TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 3016) covalent geometry : angle 0.68773 / 0.33 ( 4113) hydrogen bonds : bond 0.03999 / 2.65 ( 259) hydrogen bonds : angle 4.41607 / 3.31 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.105 Fit side-chains REVERT: A 23 LEU cc_start: 0.9106 (tp) cc_final: 0.8880 (tp) REVERT: A 51 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 326 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.7859 (mtm180) REVERT: A 458 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8331 (mp) REVERT: A 462 LEU cc_start: 0.8859 (mt) cc_final: 0.8607 (mm) outliers start: 13 outliers final: 9 residues processed: 76 average time/residue: 0.0664 time to fit residues: 6.1213 Evaluate side-chains 77 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 458 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 33 optimal weight: 0.0050 chunk 7 optimal weight: 0.0050 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 overall best weight: 0.3408 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.130746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.117360 restraints weight = 4509.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120660 restraints weight = 2202.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122943 restraints weight = 1321.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124423 restraints weight = 902.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125478 restraints weight = 672.183| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3016 Z= 0.137 Angle : 0.690 9.647 4113 Z= 0.325 Chirality : 0.041 0.165 493 Planarity : 0.005 0.040 500 Dihedral : 4.701 25.923 475 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.62 % Allowed : 24.01 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.26 (0.44), residues: 387 helix: 2.00 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.23 (0.81), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.006 0.001 TYR A 211 PHE 0.017 0.001 PHE A 348 TRP 0.005 0.001 TRP A 328 HIS 0.001 0.000 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 3016) covalent geometry : angle 0.69027 / 0.32 ( 4113) hydrogen bonds : bond 0.03904 / 2.55 ( 259) hydrogen bonds : angle 4.33745 / 3.27 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.130 Fit side-chains REVERT: A 51 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8188 (tt) REVERT: A 168 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7624 (mt) REVERT: A 458 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8288 (mp) REVERT: A 462 LEU cc_start: 0.8926 (mt) cc_final: 0.8667 (mm) outliers start: 11 outliers final: 6 residues processed: 75 average time/residue: 0.0767 time to fit residues: 6.9810 Evaluate side-chains 74 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 458 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.130213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116943 restraints weight = 4639.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120231 restraints weight = 2239.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122513 restraints weight = 1336.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123969 restraints weight = 903.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.125091 restraints weight = 674.302| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3016 Z= 0.143 Angle : 0.689 9.773 4113 Z= 0.325 Chirality : 0.041 0.163 493 Planarity : 0.005 0.041 500 Dihedral : 4.621 26.489 475 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.95 % Allowed : 22.70 % Favored : 73.36 % 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: 2.26 (0.44), residues: 387 helix: 1.98 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.11 (0.83), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 326 TYR 0.006 0.001 TYR A 211 PHE 0.017 0.001 PHE A 348 TRP 0.005 0.001 TRP A 318 HIS 0.001 0.000 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 3016) covalent geometry : angle 0.68939 / 0.33 ( 4113) hydrogen bonds : bond 0.03840 / 2.52 ( 259) hydrogen bonds : angle 4.32187 / 3.25 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.107 Fit side-chains REVERT: A 51 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8230 (tt) REVERT: A 168 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7631 (mt) REVERT: A 326 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8163 (mtm180) REVERT: A 458 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 462 LEU cc_start: 0.8948 (mt) cc_final: 0.8701 (mm) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.0680 time to fit residues: 6.0972 Evaluate side-chains 74 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 458 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.130311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116913 restraints weight = 4622.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120222 restraints weight = 2238.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122504 restraints weight = 1342.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.123995 restraints weight = 911.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125072 restraints weight = 677.745| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3016 Z= 0.142 Angle : 0.689 9.698 4113 Z= 0.325 Chirality : 0.041 0.163 493 Planarity : 0.005 0.041 500 Dihedral : 4.604 25.539 475 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.95 % Allowed : 23.68 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.27 (0.44), residues: 387 helix: 1.96 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.96 (0.84), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 326 TYR 0.006 0.001 TYR A 211 PHE 0.017 0.001 PHE A 348 TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 3016) covalent geometry : angle 0.68879 / 0.33 ( 4113) hydrogen bonds : bond 0.03816 / 2.51 ( 259) hydrogen bonds : angle 4.30999 / 3.25 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.104 Fit side-chains REVERT: A 156 ILE cc_start: 0.8612 (tt) cc_final: 0.8334 (tp) REVERT: A 168 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7625 (mt) REVERT: A 326 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8163 (mtm180) REVERT: A 458 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8270 (mp) REVERT: A 462 LEU cc_start: 0.8946 (mt) cc_final: 0.8684 (mm) outliers start: 12 outliers final: 10 residues processed: 75 average time/residue: 0.0674 time to fit residues: 6.1632 Evaluate side-chains 77 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 458 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.131494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117702 restraints weight = 4644.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121110 restraints weight = 2268.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123409 restraints weight = 1369.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124939 restraints weight = 939.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126039 restraints weight = 703.598| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3016 Z= 0.136 Angle : 0.682 9.722 4113 Z= 0.321 Chirality : 0.041 0.161 493 Planarity : 0.005 0.043 500 Dihedral : 4.599 25.580 475 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.95 % Allowed : 23.68 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.35 (0.44), residues: 387 helix: 1.97 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -0.76 (0.88), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 326 TYR 0.006 0.001 TYR A 211 PHE 0.017 0.001 PHE A 348 TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 3016) covalent geometry : angle 0.68233 / 0.32 ( 4113) hydrogen bonds : bond 0.03708 / 2.44 ( 259) hydrogen bonds : angle 4.25777 / 3.20 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.107 Fit side-chains REVERT: A 51 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8214 (tt) REVERT: A 142 GLN cc_start: 0.8578 (tt0) cc_final: 0.8343 (tt0) REVERT: A 156 ILE cc_start: 0.8595 (tt) cc_final: 0.8329 (tp) REVERT: A 168 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7621 (mt) REVERT: A 326 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8168 (mtm180) REVERT: A 458 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8268 (mp) REVERT: A 462 LEU cc_start: 0.8945 (mt) cc_final: 0.8684 (mm) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.0652 time to fit residues: 6.3402 Evaluate side-chains 81 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 458 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 0.0070 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.0070 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.140496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127598 restraints weight = 4311.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130774 restraints weight = 2133.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132991 restraints weight = 1313.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.134384 restraints weight = 901.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135462 restraints weight = 685.515| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3016 Z= 0.146 Angle : 0.688 9.741 4113 Z= 0.325 Chirality : 0.041 0.161 493 Planarity : 0.005 0.042 500 Dihedral : 4.563 25.299 475 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.95 % Allowed : 24.34 % Favored : 71.71 % 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: 2.32 (0.44), residues: 387 helix: 1.98 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.84 (0.86), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 326 TYR 0.007 0.001 TYR A 211 PHE 0.017 0.001 PHE A 348 TRP 0.006 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 3016) covalent geometry : angle 0.68826 / 0.33 ( 4113) hydrogen bonds : bond 0.03773 / 2.48 ( 259) hydrogen bonds : angle 4.27682 / 3.21 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.122 Fit side-chains REVERT: A 51 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8232 (tt) REVERT: A 156 ILE cc_start: 0.8609 (tt) cc_final: 0.8333 (tp) REVERT: A 168 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7643 (mt) REVERT: A 326 ARG cc_start: 0.8557 (ttm-80) cc_final: 0.8176 (mtm180) REVERT: A 458 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8289 (mp) REVERT: A 462 LEU cc_start: 0.8954 (mt) cc_final: 0.8679 (mm) outliers start: 12 outliers final: 9 residues processed: 77 average time/residue: 0.0592 time to fit residues: 5.5631 Evaluate side-chains 77 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 458 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.0050 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.139729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126627 restraints weight = 4391.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129917 restraints weight = 2173.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132157 restraints weight = 1319.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133636 restraints weight = 907.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134610 restraints weight = 681.769| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3016 Z= 0.151 Angle : 0.701 9.808 4113 Z= 0.331 Chirality : 0.042 0.162 493 Planarity : 0.005 0.042 500 Dihedral : 4.553 25.669 475 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.28 % Allowed : 24.34 % Favored : 71.38 % 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: 2.33 (0.44), residues: 387 helix: 1.93 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -0.60 (0.87), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 326 TYR 0.007 0.001 TYR A 211 PHE 0.017 0.001 PHE A 348 TRP 0.006 0.001 TRP A 318 HIS 0.000 0.000 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 3016) covalent geometry : angle 0.70089 / 0.33 ( 4113) hydrogen bonds : bond 0.03804 / 2.50 ( 259) hydrogen bonds : angle 4.28994 / 3.23 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 737.43 seconds wall clock time: 13 minutes 24.40 seconds (804.40 seconds total)