Starting phenix.real_space_refine on Fri May 9 15:42:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtc_36640/05_2025/8jtc_36640.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtc_36640/05_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_36640/05_2025/8jtc_36640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtc_36640/05_2025/8jtc_36640.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtc_36640/05_2025/8jtc_36640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtc_36640/05_2025/8jtc_36640.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} 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: 2.81, per 1000 atoms: 0.96 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: 0.90 Conformation dependent library (CDL) restraints added in 407.2 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: 0.28 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: 0.87 Time building geometry restraints manager: 1.04 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: 0.730 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.110 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (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 TRP 0.011 0.002 TRP A 451 HIS 0.002 0.001 HIS A 53 PHE 0.020 0.001 PHE A 348 TYR 0.016 0.001 TYR A 243 ARG 0.006 0.001 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.12408 ( 259) hydrogen bonds : angle 6.48892 ( 768) covalent geometry : bond 0.00689 ( 3016) covalent geometry : angle 0.94392 ( 4113) *********************** 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 : 0.352 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.1687 time to fit residues: 12.4922 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 : 0.324 ------------------------------------------------------------------------------- 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 32 optimal weight: 4.9990 chunk 29 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.128293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115110 restraints weight = 4483.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118513 restraints weight = 2160.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120777 restraints weight = 1280.150| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.003 0.030 3016 Z= 0.155 Angle : 0.711 9.750 4113 Z= 0.338 Chirality : 0.043 0.197 493 Planarity : 0.005 0.044 500 Dihedral : 5.225 29.352 477 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 : 2.63 % Allowed : 20.07 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.43), residues: 387 helix: 1.65 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -1.03 (0.82), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.021 0.001 PHE A 348 TYR 0.006 0.001 TYR A 433 ARG 0.005 0.001 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 259) hydrogen bonds : angle 4.73600 ( 768) covalent geometry : bond 0.00348 ( 3016) covalent geometry : angle 0.71081 ( 4113) *********************** 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 75 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.266 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 72 average time/residue: 0.1335 time to fit residues: 11.6651 Evaluate side-chains 65 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.0030 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.0770 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 overall best weight: 0.4548 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.128392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115405 restraints weight = 4430.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118681 restraints weight = 2145.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120905 restraints weight = 1275.128| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3016 Z= 0.147 Angle : 0.704 9.792 4113 Z= 0.330 Chirality : 0.042 0.193 493 Planarity : 0.005 0.039 500 Dihedral : 4.911 28.153 475 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.63 % Allowed : 22.37 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.43), residues: 387 helix: 1.89 (0.28), residues: 328 sheet: None (None), residues: 0 loop : -1.05 (0.81), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.001 0.000 HIS A 53 PHE 0.019 0.001 PHE A 348 TYR 0.007 0.001 TYR A 211 ARG 0.004 0.001 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 259) hydrogen bonds : angle 4.49932 ( 768) covalent geometry : bond 0.00328 ( 3016) covalent geometry : angle 0.70360 ( 4113) *********************** 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 75 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.410 Fit side-chains REVERT: A 326 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.7910 (mtm180) outliers start: 8 outliers final: 6 residues processed: 71 average time/residue: 0.1557 time to fit residues: 13.3678 Evaluate side-chains 69 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 265 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 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 = 0.3602 r_free = 0.3602 target = 0.141165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128703 restraints weight = 4337.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131921 restraints weight = 2156.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134058 restraints weight = 1303.949| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1226 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 : 0.691 9.829 4113 Z= 0.328 Chirality : 0.042 0.186 493 Planarity : 0.005 0.038 500 Dihedral : 4.668 27.274 475 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.43), residues: 387 helix: 1.87 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -1.02 (0.81), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 PHE 0.018 0.001 PHE A 348 TYR 0.008 0.001 TYR A 211 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 259) hydrogen bonds : angle 4.44168 ( 768) covalent geometry : bond 0.00354 ( 3016) covalent geometry : angle 0.69089 ( 4113) *********************** 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 75 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.323 Fit side-chains REVERT: A 142 GLN cc_start: 0.8635 (tt0) cc_final: 0.8411 (tt0) REVERT: A 458 ILE cc_start: 0.8534 (mt) cc_final: 0.8202 (mp) REVERT: A 462 LEU cc_start: 0.8851 (mt) cc_final: 0.8563 (mm) outliers start: 9 outliers final: 7 residues processed: 71 average time/residue: 0.1603 time to fit residues: 13.6475 Evaluate side-chains 70 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.126661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.113444 restraints weight = 4533.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116782 restraints weight = 2218.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119022 restraints weight = 1330.474| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3016 Z= 0.172 Angle : 0.712 9.959 4113 Z= 0.339 Chirality : 0.043 0.177 493 Planarity : 0.005 0.039 500 Dihedral : 4.645 27.586 475 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.43), residues: 387 helix: 1.90 (0.29), residues: 327 sheet: None (None), residues: 0 loop : -1.33 (0.80), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 PHE 0.018 0.001 PHE A 348 TYR 0.008 0.001 TYR A 211 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 259) hydrogen bonds : angle 4.43055 ( 768) covalent geometry : bond 0.00408 ( 3016) covalent geometry : angle 0.71218 ( 4113) *********************** 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 76 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.317 Fit side-chains REVERT: A 51 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8265 (tt) REVERT: A 142 GLN cc_start: 0.8647 (tt0) cc_final: 0.8437 (tt0) REVERT: A 168 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7666 (mt) REVERT: A 326 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.7835 (mtm180) REVERT: A 462 LEU cc_start: 0.8856 (mt) cc_final: 0.8567 (mm) outliers start: 11 outliers final: 8 residues processed: 73 average time/residue: 0.1575 time to fit residues: 13.8007 Evaluate side-chains 72 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.0270 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.126892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113686 restraints weight = 4602.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117039 restraints weight = 2223.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119262 restraints weight = 1326.153| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1378 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 : 0.702 9.852 4113 Z= 0.333 Chirality : 0.042 0.171 493 Planarity : 0.005 0.039 500 Dihedral : 4.650 27.202 475 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.28 % Allowed : 22.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.43), residues: 387 helix: 1.90 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.35 (0.80), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 PHE 0.018 0.001 PHE A 348 TYR 0.007 0.001 TYR A 211 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 259) hydrogen bonds : angle 4.41743 ( 768) covalent geometry : bond 0.00370 ( 3016) covalent geometry : angle 0.70153 ( 4113) *********************** 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 79 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.408 Fit side-chains REVERT: A 51 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8253 (tt) REVERT: A 168 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7663 (mt) REVERT: A 462 LEU cc_start: 0.8872 (mt) cc_final: 0.8601 (mm) outliers start: 13 outliers final: 9 residues processed: 75 average time/residue: 0.1631 time to fit residues: 14.7215 Evaluate side-chains 75 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 7 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.128873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115717 restraints weight = 4615.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119086 restraints weight = 2223.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121303 restraints weight = 1313.904| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1476 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= 0.145 Angle : 0.696 9.794 4113 Z= 0.329 Chirality : 0.041 0.174 493 Planarity : 0.005 0.039 500 Dihedral : 4.656 26.868 475 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.95 % Allowed : 23.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.43), residues: 387 helix: 1.96 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.33 (0.81), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 53 PHE 0.018 0.001 PHE A 348 TYR 0.006 0.001 TYR A 211 ARG 0.006 0.001 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 259) hydrogen bonds : angle 4.36819 ( 768) covalent geometry : bond 0.00326 ( 3016) covalent geometry : angle 0.69597 ( 4113) *********************** 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 77 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.305 Fit side-chains REVERT: A 168 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7638 (mt) REVERT: A 326 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8152 (mtm180) REVERT: A 458 ILE cc_start: 0.8566 (mt) cc_final: 0.8320 (mp) REVERT: A 462 LEU cc_start: 0.8903 (mt) cc_final: 0.8627 (mm) outliers start: 12 outliers final: 10 residues processed: 71 average time/residue: 0.1554 time to fit residues: 13.2417 Evaluate side-chains 73 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 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 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 16 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.0060 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.127976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114954 restraints weight = 4489.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118177 restraints weight = 2193.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120420 restraints weight = 1317.329| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1459 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 : 0.704 9.853 4113 Z= 0.333 Chirality : 0.042 0.172 493 Planarity : 0.005 0.039 500 Dihedral : 4.624 26.902 475 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.61 % Allowed : 22.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.43), residues: 387 helix: 1.92 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -1.22 (0.83), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 414 PHE 0.018 0.001 PHE A 348 TYR 0.007 0.001 TYR A 211 ARG 0.005 0.001 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 259) hydrogen bonds : angle 4.37543 ( 768) covalent geometry : bond 0.00370 ( 3016) covalent geometry : angle 0.70366 ( 4113) *********************** 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: 14 poor density : 65 time to evaluate : 0.317 Fit side-chains REVERT: A 142 GLN cc_start: 0.8612 (tt0) cc_final: 0.8405 (tt0) REVERT: A 156 ILE cc_start: 0.8595 (tt) cc_final: 0.8308 (tp) REVERT: A 168 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7664 (mt) REVERT: A 176 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7354 (t80) REVERT: A 326 ARG cc_start: 0.8561 (ttm-80) cc_final: 0.8147 (mtm180) REVERT: A 462 LEU cc_start: 0.8910 (mt) cc_final: 0.8633 (mm) outliers start: 14 outliers final: 11 residues processed: 74 average time/residue: 0.1648 time to fit residues: 14.5000 Evaluate side-chains 75 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 176 PHE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 232 VAL 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 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 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 23 optimal weight: 0.0170 chunk 6 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.128436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114942 restraints weight = 4498.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118341 restraints weight = 2199.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120591 restraints weight = 1320.123| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1603 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= 0.145 Angle : 0.694 9.767 4113 Z= 0.329 Chirality : 0.041 0.168 493 Planarity : 0.005 0.040 500 Dihedral : 4.585 26.570 475 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 : 3.29 % Allowed : 24.67 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.43), residues: 387 helix: 1.94 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.15 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.000 0.000 HIS A 414 PHE 0.017 0.001 PHE A 348 TYR 0.006 0.001 TYR A 211 ARG 0.005 0.001 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 259) hydrogen bonds : angle 4.34591 ( 768) covalent geometry : bond 0.00326 ( 3016) covalent geometry : angle 0.69423 ( 4113) *********************** 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 78 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.338 Fit side-chains REVERT: A 156 ILE cc_start: 0.8597 (tt) cc_final: 0.8317 (tp) REVERT: A 326 ARG cc_start: 0.8567 (ttm-80) cc_final: 0.8132 (mtm180) REVERT: A 402 MET cc_start: 0.8463 (mmt) cc_final: 0.8195 (mmm) REVERT: A 458 ILE cc_start: 0.8566 (mt) cc_final: 0.8312 (mp) REVERT: A 462 LEU cc_start: 0.8909 (mt) cc_final: 0.8626 (mm) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 0.1738 time to fit residues: 15.2358 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 : 0.326 ------------------------------------------------------------------------------- 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 238 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 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 = 0.3334 r_free = 0.3334 target = 0.121361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107419 restraints weight = 4463.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110661 restraints weight = 2233.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.112901 restraints weight = 1369.684| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3016 Z= 0.164 Angle : 0.711 9.867 4113 Z= 0.338 Chirality : 0.042 0.172 493 Planarity : 0.005 0.039 500 Dihedral : 4.559 27.119 475 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.62 % Allowed : 25.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.43), residues: 387 helix: 1.92 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.18 (0.83), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.000 0.000 HIS A 414 PHE 0.018 0.001 PHE A 348 TYR 0.008 0.001 TYR A 243 ARG 0.006 0.001 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 259) hydrogen bonds : angle 4.38018 ( 768) covalent geometry : bond 0.00388 ( 3016) covalent geometry : angle 0.71073 ( 4113) ********************** 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 74 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.344 Fit side-chains REVERT: A 51 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8243 (tt) REVERT: A 156 ILE cc_start: 0.8600 (tt) cc_final: 0.8334 (tp) REVERT: A 176 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7394 (t80) REVERT: A 462 LEU cc_start: 0.8971 (mt) cc_final: 0.8711 (mm) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.1624 time to fit residues: 13.5442 Evaluate side-chains 72 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 176 PHE Chi-restraints excluded: chain A residue 238 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.0170 chunk 23 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.140518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.127158 restraints weight = 4287.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130431 restraints weight = 2154.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.132663 restraints weight = 1327.262| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1700 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= 0.138 Angle : 0.698 9.744 4113 Z= 0.329 Chirality : 0.041 0.174 493 Planarity : 0.005 0.042 500 Dihedral : 4.582 25.566 475 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.63 % Allowed : 25.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.44), residues: 387 helix: 1.99 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -1.07 (0.86), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.001 0.000 HIS A 53 PHE 0.017 0.001 PHE A 348 TYR 0.006 0.001 TYR A 211 ARG 0.006 0.001 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 259) hydrogen bonds : angle 4.30987 ( 768) covalent geometry : bond 0.00302 ( 3016) covalent geometry : angle 0.69755 ( 4113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1288.52 seconds wall clock time: 23 minutes 11.83 seconds (1391.83 seconds total)