Starting phenix.real_space_refine on Fri Aug 22 13:04:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtc_36640/08_2025/8jtc_36640.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtc_36640/08_2025/8jtc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jtc_36640/08_2025/8jtc_36640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtc_36640/08_2025/8jtc_36640.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtc_36640/08_2025/8jtc_36640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtc_36640/08_2025/8jtc_36640.cif" } 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-2.0-5787/lib/python3.9/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: 1.03, per 1000 atoms: 0.35 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: 0.30 Conformation dependent library (CDL) restraints added in 122.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.10 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: 0.51 Time building geometry restraints manager: 0.40 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: 1.030 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: 5.330 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 aren 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 covalent geometry : bond 0.00689 ( 3016) covalent geometry : angle 0.94392 ( 4113) hydrogen bonds : bond 0.12408 ( 259) hydrogen bonds : angle 6.48892 ( 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 : 0.107 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.0756 time to fit residues: 5.6075 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 : 0.133 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 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 414 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.129422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.116744 restraints weight = 4528.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119972 restraints weight = 2208.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122164 restraints weight = 1319.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123617 restraints weight = 890.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124722 restraints weight = 660.266| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.0784 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= 0.164 Angle : 0.718 9.806 4113 Z= 0.341 Chirality : 0.043 0.197 493 Planarity : 0.005 0.044 500 Dihedral : 5.229 29.646 477 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.63 % Allowed : 19.74 % Favored : 77.63 % 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 aren not related in a simple way. whole: 1.84 (0.42), residues: 387 helix: 1.64 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -1.06 (0.81), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.006 0.001 TYR A 211 PHE 0.021 0.001 PHE A 348 TRP 0.010 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 3016) covalent geometry : angle 0.71777 ( 4113) hydrogen bonds : bond 0.04263 ( 259) hydrogen bonds : angle 4.74253 ( 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 : 0.125 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.0778 time to fit residues: 6.9179 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 : 0.121 ------------------------------------------------------------------------------- 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: 0.6980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.126775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113579 restraints weight = 4583.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116924 restraints weight = 2201.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119061 restraints weight = 1307.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120620 restraints weight = 899.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121199 restraints weight = 664.142| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3016 Z= 0.168 Angle : 0.712 9.934 4113 Z= 0.338 Chirality : 0.043 0.188 493 Planarity : 0.005 0.038 500 Dihedral : 5.063 29.620 477 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.96 % Allowed : 21.71 % Favored : 75.33 % 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 aren not related in a simple way. whole: 2.11 (0.43), residues: 387 helix: 1.85 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -1.13 (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 0.019 0.001 PHE A 348 TRP 0.006 0.001 TRP A 318 HIS 0.000 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 3016) covalent geometry : angle 0.71195 ( 4113) hydrogen bonds : bond 0.04230 ( 259) hydrogen bonds : angle 4.53792 ( 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 74 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.142 Fit side-chains REVERT: A 326 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.7936 (mtm180) outliers start: 9 outliers final: 6 residues processed: 70 average time/residue: 0.0696 time to fit residues: 5.8882 Evaluate side-chains 67 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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: 0.6980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.127557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.114503 restraints weight = 4505.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117768 restraints weight = 2195.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.120058 restraints weight = 1307.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121524 restraints weight = 880.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122575 restraints weight = 653.159| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.004 0.031 3016 Z= 0.156 Angle : 0.697 9.831 4113 Z= 0.330 Chirality : 0.042 0.184 493 Planarity : 0.005 0.038 500 Dihedral : 4.745 27.436 475 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.96 % Allowed : 23.03 % Favored : 74.01 % 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 aren not related in a simple way. whole: 2.15 (0.43), residues: 387 helix: 1.88 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -1.16 (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 0.018 0.001 PHE A 348 TRP 0.006 0.001 TRP A 318 HIS 0.000 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3016) covalent geometry : angle 0.69660 ( 4113) hydrogen bonds : bond 0.04052 ( 259) hydrogen bonds : angle 4.46470 ( 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: 9 poor density : 68 time to evaluate : 0.115 Fit side-chains REVERT: A 458 ILE cc_start: 0.8502 (mt) cc_final: 0.8273 (mt) REVERT: A 462 LEU cc_start: 0.8840 (mt) cc_final: 0.8568 (mm) outliers start: 9 outliers final: 7 residues processed: 73 average time/residue: 0.0731 time to fit residues: 6.4214 Evaluate side-chains 72 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.0050 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.129596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116369 restraints weight = 4493.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119703 restraints weight = 2185.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121907 restraints weight = 1303.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123363 restraints weight = 889.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124395 restraints weight = 666.946| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3016 Z= 0.136 Angle : 0.677 9.731 4113 Z= 0.322 Chirality : 0.041 0.175 493 Planarity : 0.005 0.040 500 Dihedral : 4.720 26.959 475 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.62 % Allowed : 23.36 % Favored : 73.03 % 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 aren not related in a simple way. whole: 2.30 (0.43), residues: 387 helix: 2.03 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.28 (0.81), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.007 0.001 TYR A 211 PHE 0.017 0.001 PHE A 348 TRP 0.005 0.001 TRP A 328 HIS 0.000 0.000 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3016) covalent geometry : angle 0.67725 ( 4113) hydrogen bonds : bond 0.03843 ( 259) hydrogen bonds : angle 4.36285 ( 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: 11 poor density : 70 time to evaluate : 0.115 Fit side-chains REVERT: A 23 LEU cc_start: 0.9088 (tp) cc_final: 0.8855 (tp) REVERT: A 51 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8234 (tt) REVERT: A 326 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.7848 (mtm180) REVERT: A 458 ILE cc_start: 0.8540 (mt) cc_final: 0.8287 (mt) REVERT: A 462 LEU cc_start: 0.8849 (mt) cc_final: 0.8558 (mm) outliers start: 11 outliers final: 8 residues processed: 78 average time/residue: 0.0644 time to fit residues: 6.0923 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 : 0.097 ------------------------------------------------------------------------------- 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 300 SER Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.0020 chunk 33 optimal weight: 0.2980 chunk 7 optimal weight: 0.0570 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.0470 chunk 12 optimal weight: 0.7980 overall best weight: 0.2004 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.133352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119515 restraints weight = 4504.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122924 restraints weight = 2222.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125179 restraints weight = 1354.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126683 restraints weight = 936.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127774 restraints weight = 708.801| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3016 Z= 0.128 Angle : 0.671 9.608 4113 Z= 0.317 Chirality : 0.041 0.157 493 Planarity : 0.005 0.043 500 Dihedral : 4.763 24.920 475 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.64 % Allowed : 25.99 % 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 aren not related in a simple way. whole: 2.38 (0.44), residues: 387 helix: 2.03 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -0.93 (0.85), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.005 0.001 TYR A 408 PHE 0.016 0.001 PHE A 348 TRP 0.006 0.001 TRP A 328 HIS 0.001 0.000 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3016) covalent geometry : angle 0.67099 ( 4113) hydrogen bonds : bond 0.03732 ( 259) hydrogen bonds : angle 4.28176 ( 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 80 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.116 Fit side-chains REVERT: A 23 LEU cc_start: 0.9066 (tp) cc_final: 0.8839 (tp) REVERT: A 242 LEU cc_start: 0.8783 (tt) cc_final: 0.8503 (tt) REVERT: A 326 ARG cc_start: 0.8325 (ttm-80) cc_final: 0.7759 (mtm180) REVERT: A 458 ILE cc_start: 0.8546 (mt) cc_final: 0.8274 (mt) REVERT: A 462 LEU cc_start: 0.8830 (mt) cc_final: 0.8531 (mm) outliers start: 5 outliers final: 3 residues processed: 78 average time/residue: 0.0715 time to fit residues: 6.7264 Evaluate side-chains 72 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 0.0470 chunk 5 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.130398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116824 restraints weight = 4643.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120242 restraints weight = 2258.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122543 restraints weight = 1349.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123991 restraints weight = 915.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125082 restraints weight = 689.009| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3016 Z= 0.147 Angle : 0.685 9.806 4113 Z= 0.325 Chirality : 0.042 0.159 493 Planarity : 0.005 0.041 500 Dihedral : 4.584 26.479 475 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.09 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 aren not related in a simple way. whole: 2.37 (0.44), residues: 387 helix: 2.01 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -0.90 (0.86), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.007 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 covalent geometry : bond 0.00335 ( 3016) covalent geometry : angle 0.68523 ( 4113) hydrogen bonds : bond 0.03796 ( 259) hydrogen bonds : angle 4.31142 ( 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 82 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.110 Fit side-chains REVERT: A 23 LEU cc_start: 0.9073 (tp) cc_final: 0.8847 (tp) REVERT: A 168 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7619 (mt) REVERT: A 458 ILE cc_start: 0.8551 (mt) cc_final: 0.8280 (mt) REVERT: A 462 LEU cc_start: 0.8848 (mt) cc_final: 0.8549 (mm) outliers start: 12 outliers final: 10 residues processed: 77 average time/residue: 0.0715 time to fit residues: 6.6309 Evaluate side-chains 78 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.129984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116090 restraints weight = 4646.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119483 restraints weight = 2300.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121750 restraints weight = 1400.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.123298 restraints weight = 966.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124405 restraints weight = 725.642| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3016 Z= 0.156 Angle : 0.701 9.828 4113 Z= 0.333 Chirality : 0.042 0.163 493 Planarity : 0.005 0.039 500 Dihedral : 4.575 25.839 475 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.28 % Allowed : 24.01 % 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 aren not related in a simple way. whole: 2.29 (0.43), residues: 387 helix: 1.97 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -0.97 (0.85), residues: 60 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 0.005 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3016) covalent geometry : angle 0.70111 ( 4113) hydrogen bonds : bond 0.03852 ( 259) hydrogen bonds : angle 4.32426 ( 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 79 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.110 Fit side-chains REVERT: A 156 ILE cc_start: 0.8624 (tt) cc_final: 0.8344 (tp) REVERT: A 168 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7657 (mt) REVERT: A 326 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8179 (mtm180) REVERT: A 458 ILE cc_start: 0.8528 (mt) cc_final: 0.8266 (mt) REVERT: A 462 LEU cc_start: 0.8861 (mt) cc_final: 0.8589 (mm) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.0713 time to fit residues: 6.3818 Evaluate side-chains 76 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 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 168 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 THR 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 323 MET Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.0050 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.123755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.109802 restraints weight = 4490.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113070 restraints weight = 2225.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115384 restraints weight = 1346.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116971 restraints weight = 920.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117969 restraints weight = 683.114| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3016 Z= 0.140 Angle : 0.689 9.770 4113 Z= 0.326 Chirality : 0.041 0.164 493 Planarity : 0.005 0.041 500 Dihedral : 4.590 25.852 475 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.95 % Allowed : 25.33 % Favored : 70.72 % 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 aren not related in a simple way. whole: 2.35 (0.44), residues: 387 helix: 2.00 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -0.89 (0.86), 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 414 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3016) covalent geometry : angle 0.68944 ( 4113) hydrogen bonds : bond 0.03748 ( 259) hydrogen bonds : angle 4.29091 ( 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 82 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.108 Fit side-chains REVERT: A 23 LEU cc_start: 0.9057 (tp) cc_final: 0.8811 (tp) REVERT: A 156 ILE cc_start: 0.8614 (tt) cc_final: 0.8353 (tp) REVERT: A 168 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7622 (mt) REVERT: A 326 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8167 (mtm180) REVERT: A 458 ILE cc_start: 0.8537 (mt) cc_final: 0.8277 (mt) REVERT: A 462 LEU cc_start: 0.8866 (mt) cc_final: 0.8578 (mm) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 0.0684 time to fit residues: 6.5205 Evaluate side-chains 79 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 198 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 31 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 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 = 0.3611 r_free = 0.3611 target = 0.141080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128183 restraints weight = 4289.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131423 restraints weight = 2111.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133633 restraints weight = 1279.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134999 restraints weight = 877.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136083 restraints weight = 666.150| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3016 Z= 0.136 Angle : 0.685 9.668 4113 Z= 0.324 Chirality : 0.041 0.157 493 Planarity : 0.005 0.042 500 Dihedral : 4.594 24.962 475 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.63 % Allowed : 26.32 % Favored : 71.05 % 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 aren not related in a simple way. whole: 2.41 (0.44), residues: 387 helix: 2.02 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -0.71 (0.88), 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 0.001 0.000 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3016) covalent geometry : angle 0.68493 ( 4113) hydrogen bonds : bond 0.03674 ( 259) hydrogen bonds : angle 4.26429 ( 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 84 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.113 Fit side-chains REVERT: A 23 LEU cc_start: 0.9081 (tp) cc_final: 0.8836 (tp) REVERT: A 142 GLN cc_start: 0.8534 (tt0) cc_final: 0.8297 (tt0) REVERT: A 156 ILE cc_start: 0.8588 (tt) cc_final: 0.8331 (tp) REVERT: A 168 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7650 (mt) REVERT: A 242 LEU cc_start: 0.8778 (tt) cc_final: 0.8542 (tt) REVERT: A 326 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.8237 (mtm180) REVERT: A 458 ILE cc_start: 0.8613 (mt) cc_final: 0.8373 (mt) REVERT: A 462 LEU cc_start: 0.8891 (mt) cc_final: 0.8615 (mm) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.0690 time to fit residues: 6.8234 Evaluate side-chains 76 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 238 PHE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.139707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126576 restraints weight = 4380.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129804 restraints weight = 2165.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131997 restraints weight = 1327.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133431 restraints weight = 923.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134394 restraints weight = 702.651| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3016 Z= 0.154 Angle : 0.708 9.866 4113 Z= 0.336 Chirality : 0.042 0.160 493 Planarity : 0.005 0.042 500 Dihedral : 4.560 26.200 475 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.29 % Allowed : 25.99 % Favored : 70.72 % 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 aren not related in a simple way. whole: 2.48 (0.44), residues: 387 helix: 2.14 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.75 (0.83), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 326 TYR 0.008 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 covalent geometry : bond 0.00358 ( 3016) covalent geometry : angle 0.70843 ( 4113) hydrogen bonds : bond 0.03840 ( 259) hydrogen bonds : angle 4.31348 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 752.52 seconds wall clock time: 13 minutes 36.03 seconds (816.03 seconds total)