Starting phenix.real_space_refine on Thu Jul 2 00:00:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wx9_66339/07_2026/9wx9_66339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wx9_66339/07_2026/9wx9_66339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wx9_66339/07_2026/9wx9_66339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wx9_66339/07_2026/9wx9_66339.map" model { file = "/net/cci-nas-00/data/ceres_data/9wx9_66339/07_2026/9wx9_66339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wx9_66339/07_2026/9wx9_66339.cif" } resolution = 2.84 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= -0.004 sd= 0.147 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2857 2.51 5 N 657 2.21 5 O 715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4265 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4263 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 26, 'TRANS': 513} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Chain breaks: 2 Time building chain proxies: 0.92, per 1000 atoms: 0.22 Number of scatterers: 4265 At special positions: 0 Unit cell: (81.092, 68.288, 81.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 1 11.00 O 715 8.00 N 657 7.00 C 2857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 166 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 103.0 milliseconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 79.6% alpha, 0.4% 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 40 through 52 removed outlier: 3.536A pdb=" N LEU A 44 " --> pdb=" O TRP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.502A pdb=" N ASN A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 72 through 86 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 86 through 102 removed outlier: 3.547A pdb=" N LEU A 90 " --> pdb=" O CYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.599A pdb=" N TRP A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 115 through 147 removed outlier: 3.993A pdb=" N GLY A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 4.232A pdb=" N HIS A 156 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 214 through 234 Processing helix chain 'A' and resid 247 through 264 removed outlier: 3.515A pdb=" N THR A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.042A pdb=" N GLY A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.791A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 removed outlier: 4.242A pdb=" N TRP A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 318 through 353 Processing helix chain 'A' and resid 365 through 376 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 380 through 415 removed outlier: 3.564A pdb=" N TRP A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 439 Processing helix chain 'A' and resid 440 through 443 removed outlier: 3.791A pdb=" N THR A 443 " --> pdb=" O ILE A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.656A pdb=" N TRP A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 532 through 561 removed outlier: 3.839A pdb=" N SER A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.514A pdb=" N TYR A 591 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 592 " --> pdb=" O GLY A 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 588 through 592' Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 526 288 hydrogen bonds defined for protein. 843 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: 0.56 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1242 1.34 - 1.46: 1015 1.46 - 1.58: 2085 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 4396 Sorted by residual: bond pdb=" N GLN A 522 " pdb=" CA GLN A 522 " ideal model delta sigma weight residual 1.462 1.498 -0.035 1.05e-02 9.07e+03 1.14e+01 bond pdb=" N ILE A 325 " pdb=" CA ILE A 325 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" N PHE A 249 " pdb=" CA PHE A 249 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.78e+00 bond pdb=" N TYR A 371 " pdb=" CA TYR A 371 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.83e+00 bond pdb=" N VAL A 344 " pdb=" CA VAL A 344 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.81e+00 ... (remaining 4391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 5513 1.52 - 3.05: 378 3.05 - 4.57: 80 4.57 - 6.10: 19 6.10 - 7.62: 3 Bond angle restraints: 5993 Sorted by residual: angle pdb=" N GLY A 240 " pdb=" CA GLY A 240 " pdb=" C GLY A 240 " ideal model delta sigma weight residual 115.30 108.25 7.05 1.44e+00 4.82e-01 2.40e+01 angle pdb=" N LYS A 361 " pdb=" CA LYS A 361 " pdb=" C LYS A 361 " ideal model delta sigma weight residual 113.18 107.93 5.25 1.21e+00 6.83e-01 1.89e+01 angle pdb=" CA SER A 298 " pdb=" C SER A 298 " pdb=" O SER A 298 " ideal model delta sigma weight residual 120.82 116.57 4.25 1.05e+00 9.07e-01 1.64e+01 angle pdb=" N VAL A 243 " pdb=" CA VAL A 243 " pdb=" C VAL A 243 " ideal model delta sigma weight residual 112.83 108.89 3.94 9.90e-01 1.02e+00 1.58e+01 angle pdb=" CA GLY A 396 " pdb=" C GLY A 396 " pdb=" O GLY A 396 " ideal model delta sigma weight residual 120.66 116.76 3.90 1.06e+00 8.90e-01 1.36e+01 ... (remaining 5988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 2107 14.38 - 28.75: 251 28.75 - 43.13: 99 43.13 - 57.50: 32 57.50 - 71.88: 7 Dihedral angle restraints: 2496 sinusoidal: 946 harmonic: 1550 Sorted by residual: dihedral pdb=" CA TRP A 109 " pdb=" C TRP A 109 " pdb=" N LYS A 110 " pdb=" CA LYS A 110 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CG ARG A 587 " pdb=" CD ARG A 587 " pdb=" NE ARG A 587 " pdb=" CZ ARG A 587 " ideal model delta sinusoidal sigma weight residual 180.00 135.81 44.19 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG A 321 " pdb=" CD ARG A 321 " pdb=" NE ARG A 321 " pdb=" CZ ARG A 321 " ideal model delta sinusoidal sigma weight residual -180.00 -137.50 -42.50 2 1.50e+01 4.44e-03 9.74e+00 ... (remaining 2493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 531 0.056 - 0.113: 113 0.113 - 0.169: 24 0.169 - 0.226: 4 0.226 - 0.282: 2 Chirality restraints: 674 Sorted by residual: chirality pdb=" CA VAL A 242 " pdb=" N VAL A 242 " pdb=" C VAL A 242 " pdb=" CB VAL A 242 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA VAL A 243 " pdb=" N VAL A 243 " pdb=" C VAL A 243 " pdb=" CB VAL A 243 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA VAL A 476 " pdb=" N VAL A 476 " pdb=" C VAL A 476 " pdb=" CB VAL A 476 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 671 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 236 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C VAL A 236 " -0.059 2.00e-02 2.50e+03 pdb=" O VAL A 236 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS A 237 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 522 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 523 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 471 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C LEU A 471 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A 471 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 472 " -0.015 2.00e-02 2.50e+03 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 437 2.75 - 3.29: 4407 3.29 - 3.82: 7631 3.82 - 4.36: 9467 4.36 - 4.90: 15643 Nonbonded interactions: 37585 Sorted by model distance: nonbonded pdb=" OG SER A 147 " pdb=" OG SER A 385 " model vdw 2.210 3.040 nonbonded pdb=" O ALA A 84 " pdb=" OH TYR A 497 " model vdw 2.254 3.040 nonbonded pdb=" OG SER A 298 " pdb="NA NA A 701 " model vdw 2.355 3.210 nonbonded pdb=" O LEU A 378 " pdb=" OG SER A 381 " model vdw 2.359 3.040 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 536 " model vdw 2.382 3.040 ... (remaining 37580 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 individual isotropic 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: 1.470 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: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.890 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 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 : 0.006 0.057 4397 Z= 0.398 Angle : 0.869 7.622 5995 Z= 0.593 Chirality : 0.052 0.282 674 Planarity : 0.006 0.065 726 Dihedral : 15.596 71.880 1511 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 18.98 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.36), residues: 536 helix: 0.84 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.57 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.016 0.002 TYR A 132 PHE 0.015 0.001 PHE A 309 TRP 0.027 0.002 TRP A 215 HIS 0.006 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.40 ( 4396) covalent geometry : angle 0.86863 / 0.59 ( 5993) SS BOND : bond 0.00332 / 0.17 ( 1) SS BOND : angle 0.60315 / 0.33 ( 2) hydrogen bonds : bond 0.12510 / 8.29 ( 288) hydrogen bonds : angle 6.13938 / 4.26 ( 843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.115 Fit side-chains REVERT: A 94 GLU cc_start: 0.6849 (tt0) cc_final: 0.6647 (tt0) REVERT: A 289 ILE cc_start: 0.6519 (mt) cc_final: 0.6144 (mt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3368 time to fit residues: 34.5696 Evaluate side-chains 71 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.178438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.156365 restraints weight = 4827.095| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.43 r_work: 0.3550 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4397 Z= 0.175 Angle : 0.695 9.100 5995 Z= 0.346 Chirality : 0.044 0.372 674 Planarity : 0.005 0.051 726 Dihedral : 4.308 21.425 584 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.86 % Allowed : 19.65 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.35), residues: 536 helix: 1.58 (0.26), residues: 370 sheet: None (None), residues: 0 loop : -1.03 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 587 TYR 0.018 0.002 TYR A 143 PHE 0.020 0.002 PHE A 91 TRP 0.028 0.002 TRP A 534 HIS 0.011 0.002 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 4396) covalent geometry : angle 0.69365 / 0.35 ( 5993) SS BOND : bond 0.01158 / 0.61 ( 1) SS BOND : angle 2.43728 / 1.31 ( 2) hydrogen bonds : bond 0.04654 / 3.27 ( 288) hydrogen bonds : angle 4.62537 / 3.22 ( 843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 167 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6599 (mt) REVERT: A 212 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.5981 (pp20) REVERT: A 230 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7486 (mt) REVERT: A 290 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6406 (tp30) REVERT: A 322 ASP cc_start: 0.6703 (m-30) cc_final: 0.6398 (m-30) REVERT: A 332 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6815 (mt) REVERT: A 585 GLU cc_start: 0.7283 (mp0) cc_final: 0.7080 (pm20) outliers start: 22 outliers final: 3 residues processed: 92 average time/residue: 0.3898 time to fit residues: 37.5403 Evaluate side-chains 71 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 590 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 30 optimal weight: 0.0370 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.155738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.131408 restraints weight = 4627.708| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.46 r_work: 0.3275 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4397 Z= 0.198 Angle : 0.613 7.723 5995 Z= 0.313 Chirality : 0.041 0.198 674 Planarity : 0.005 0.045 726 Dihedral : 3.964 18.040 584 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.08 % Allowed : 18.54 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.36), residues: 536 helix: 1.99 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -0.71 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 587 TYR 0.015 0.002 TYR A 132 PHE 0.013 0.001 PHE A 91 TRP 0.031 0.002 TRP A 534 HIS 0.009 0.002 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.20 ( 4396) covalent geometry : angle 0.60962 / 0.31 ( 5993) SS BOND : bond 0.01123 / 0.59 ( 1) SS BOND : angle 3.50806 / 1.85 ( 2) hydrogen bonds : bond 0.04678 / 3.26 ( 288) hydrogen bonds : angle 4.35868 / 3.06 ( 843) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.093 Fit side-chains REVERT: A 135 MET cc_start: 0.8954 (tpt) cc_final: 0.8212 (tpt) REVERT: A 192 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8408 (mt-10) REVERT: A 212 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6444 (pp20) REVERT: A 298 SER cc_start: 0.8810 (t) cc_final: 0.8587 (m) REVERT: A 332 ILE cc_start: 0.8128 (mp) cc_final: 0.7851 (mt) REVERT: A 434 MET cc_start: 0.8102 (mtt) cc_final: 0.7708 (mtt) REVERT: A 514 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6311 (mtt) outliers start: 23 outliers final: 6 residues processed: 89 average time/residue: 0.3340 time to fit residues: 31.2943 Evaluate side-chains 75 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 514 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 23 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.139903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.114861 restraints weight = 4518.673| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.49 r_work: 0.3084 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.7595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4397 Z= 0.168 Angle : 0.610 7.313 5995 Z= 0.303 Chirality : 0.042 0.174 674 Planarity : 0.004 0.038 726 Dihedral : 4.091 18.953 584 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.64 % Allowed : 20.09 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.35), residues: 536 helix: 1.85 (0.25), residues: 373 sheet: None (None), residues: 0 loop : -0.59 (0.49), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 475 TYR 0.019 0.002 TYR A 132 PHE 0.012 0.002 PHE A 80 TRP 0.032 0.002 TRP A 534 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 4396) covalent geometry : angle 0.60913 / 0.30 ( 5993) SS BOND : bond 0.00242 / 0.13 ( 1) SS BOND : angle 1.52799 / 0.81 ( 2) hydrogen bonds : bond 0.04704 / 3.28 ( 288) hydrogen bonds : angle 4.40421 / 3.09 ( 843) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.096 Fit side-chains REVERT: A 212 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7806 (mm-30) REVERT: A 332 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7973 (mt) REVERT: A 434 MET cc_start: 0.8287 (mtt) cc_final: 0.7958 (mtt) REVERT: A 530 ARG cc_start: 0.7681 (mmt90) cc_final: 0.7446 (mmt-90) REVERT: A 570 GLN cc_start: 0.5846 (tp40) cc_final: 0.5381 (mt0) outliers start: 21 outliers final: 3 residues processed: 90 average time/residue: 0.3719 time to fit residues: 34.9769 Evaluate side-chains 74 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 584 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 0.0470 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.132706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.107657 restraints weight = 4585.641| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.47 r_work: 0.3050 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.8318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4397 Z= 0.143 Angle : 0.546 8.092 5995 Z= 0.272 Chirality : 0.041 0.191 674 Planarity : 0.004 0.035 726 Dihedral : 3.925 18.427 584 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.09 % Allowed : 21.63 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.36), residues: 536 helix: 2.14 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.26 (0.51), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.018 0.002 TYR A 132 PHE 0.011 0.001 PHE A 91 TRP 0.016 0.001 TRP A 215 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 4396) covalent geometry : angle 0.54492 / 0.27 ( 5993) SS BOND : bond 0.00464 / 0.24 ( 1) SS BOND : angle 1.98745 / 1.05 ( 2) hydrogen bonds : bond 0.04469 / 3.14 ( 288) hydrogen bonds : angle 4.32496 / 3.03 ( 843) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.156 Fit side-chains REVERT: A 82 MET cc_start: 0.8961 (mmm) cc_final: 0.8623 (mpm) REVERT: A 212 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7921 (mm-30) REVERT: A 332 ILE cc_start: 0.8363 (mp) cc_final: 0.7974 (mt) REVERT: A 380 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8087 (mp) REVERT: A 570 GLN cc_start: 0.6319 (tp40) cc_final: 0.5891 (mt0) outliers start: 14 outliers final: 4 residues processed: 88 average time/residue: 0.4614 time to fit residues: 42.3526 Evaluate side-chains 79 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 537 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.129605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.104966 restraints weight = 4688.968| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.47 r_work: 0.2958 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.8932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4397 Z= 0.146 Angle : 0.557 7.659 5995 Z= 0.277 Chirality : 0.041 0.202 674 Planarity : 0.004 0.033 726 Dihedral : 4.007 18.785 584 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.42 % Allowed : 20.97 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.36), residues: 536 helix: 2.17 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.11 (0.51), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.019 0.002 TYR A 132 PHE 0.012 0.001 PHE A 460 TRP 0.017 0.001 TRP A 534 HIS 0.003 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 4396) covalent geometry : angle 0.55617 / 0.28 ( 5993) SS BOND : bond 0.00404 / 0.21 ( 1) SS BOND : angle 2.15473 / 1.13 ( 2) hydrogen bonds : bond 0.04479 / 3.14 ( 288) hydrogen bonds : angle 4.36139 / 3.05 ( 843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.169 Fit side-chains REVERT: A 81 LEU cc_start: 0.8401 (mt) cc_final: 0.8101 (mt) REVERT: A 82 MET cc_start: 0.8841 (mmm) cc_final: 0.8551 (mpm) REVERT: A 93 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8387 (tp) REVERT: A 212 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: A 332 ILE cc_start: 0.8401 (mp) cc_final: 0.8007 (mt) REVERT: A 380 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8359 (mp) REVERT: A 480 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: A 499 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7095 (mtt-85) REVERT: A 503 LEU cc_start: 0.8761 (mm) cc_final: 0.8476 (mt) REVERT: A 525 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7980 (pt0) REVERT: A 570 GLN cc_start: 0.6438 (tp40) cc_final: 0.6158 (mt0) outliers start: 20 outliers final: 7 residues processed: 98 average time/residue: 0.4000 time to fit residues: 41.0006 Evaluate side-chains 92 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 14 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.128520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.104253 restraints weight = 4656.072| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.46 r_work: 0.2946 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.9238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4397 Z= 0.138 Angle : 0.555 7.824 5995 Z= 0.273 Chirality : 0.041 0.261 674 Planarity : 0.004 0.034 726 Dihedral : 3.973 18.781 584 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 5.96 % Allowed : 20.97 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.36), residues: 536 helix: 2.30 (0.26), residues: 371 sheet: None (None), residues: 0 loop : -0.15 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 530 TYR 0.018 0.002 TYR A 132 PHE 0.011 0.001 PHE A 389 TRP 0.025 0.001 TRP A 534 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 4396) covalent geometry : angle 0.55461 / 0.27 ( 5993) SS BOND : bond 0.00209 / 0.11 ( 1) SS BOND : angle 1.76565 / 0.93 ( 2) hydrogen bonds : bond 0.04422 / 3.10 ( 288) hydrogen bonds : angle 4.31192 / 3.02 ( 843) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.155 Fit side-chains REVERT: A 82 MET cc_start: 0.8777 (mmm) cc_final: 0.8526 (mmp) REVERT: A 212 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: A 237 LYS cc_start: 0.5227 (mttt) cc_final: 0.4531 (tppp) REVERT: A 332 ILE cc_start: 0.8393 (mp) cc_final: 0.8000 (mt) REVERT: A 380 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8445 (mp) REVERT: A 480 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7402 (mp10) REVERT: A 499 ARG cc_start: 0.7676 (mtm110) cc_final: 0.7182 (mtt-85) REVERT: A 503 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8492 (mt) REVERT: A 537 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7667 (tm) REVERT: A 555 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7204 (tm) REVERT: A 570 GLN cc_start: 0.6551 (tp40) cc_final: 0.6314 (mt0) outliers start: 27 outliers final: 9 residues processed: 95 average time/residue: 0.4672 time to fit residues: 46.2035 Evaluate side-chains 92 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.125098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.101176 restraints weight = 4619.140| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.45 r_work: 0.2891 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.9611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4397 Z= 0.159 Angle : 0.581 8.204 5995 Z= 0.288 Chirality : 0.042 0.268 674 Planarity : 0.004 0.033 726 Dihedral : 4.079 18.868 584 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.74 % Allowed : 20.97 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.36), residues: 536 helix: 2.12 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.12 (0.51), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 560 TYR 0.019 0.002 TYR A 132 PHE 0.011 0.001 PHE A 389 TRP 0.031 0.002 TRP A 534 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 4396) covalent geometry : angle 0.57968 / 0.29 ( 5993) SS BOND : bond 0.00448 / 0.24 ( 1) SS BOND : angle 2.46437 / 1.30 ( 2) hydrogen bonds : bond 0.04655 / 3.25 ( 288) hydrogen bonds : angle 4.40243 / 3.09 ( 843) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.165 Fit side-chains REVERT: A 82 MET cc_start: 0.8782 (mmm) cc_final: 0.8534 (mmp) REVERT: A 191 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8107 (tp30) REVERT: A 212 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7911 (mm-30) REVERT: A 237 LYS cc_start: 0.5426 (mttt) cc_final: 0.4719 (tppp) REVERT: A 332 ILE cc_start: 0.8377 (mp) cc_final: 0.7981 (mt) REVERT: A 348 MET cc_start: 0.8341 (mtp) cc_final: 0.7969 (mtp) REVERT: A 351 GLU cc_start: 0.8200 (tp30) cc_final: 0.7881 (tp30) REVERT: A 380 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8402 (mp) REVERT: A 480 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: A 499 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7194 (mtt-85) REVERT: A 503 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8332 (mt) REVERT: A 555 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7185 (tm) REVERT: A 559 LEU cc_start: 0.8289 (mt) cc_final: 0.8044 (mm) outliers start: 26 outliers final: 9 residues processed: 94 average time/residue: 0.4812 time to fit residues: 47.1466 Evaluate side-chains 91 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 GLN A 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.122883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.100350 restraints weight = 4677.467| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.31 r_work: 0.2860 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.9856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4397 Z= 0.160 Angle : 0.589 8.415 5995 Z= 0.288 Chirality : 0.043 0.287 674 Planarity : 0.004 0.034 726 Dihedral : 4.104 18.927 584 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.64 % Allowed : 21.41 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.36), residues: 536 helix: 2.10 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.07 (0.51), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 560 TYR 0.019 0.002 TYR A 132 PHE 0.020 0.001 PHE A 460 TRP 0.030 0.002 TRP A 534 HIS 0.003 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 4396) covalent geometry : angle 0.58829 / 0.29 ( 5993) SS BOND : bond 0.00328 / 0.17 ( 1) SS BOND : angle 2.13476 / 1.13 ( 2) hydrogen bonds : bond 0.04645 / 3.25 ( 288) hydrogen bonds : angle 4.44483 / 3.11 ( 843) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.156 Fit side-chains REVERT: A 191 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8195 (tp30) REVERT: A 237 LYS cc_start: 0.5761 (mttt) cc_final: 0.5076 (tppp) REVERT: A 332 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8217 (mt) REVERT: A 351 GLU cc_start: 0.8360 (tp30) cc_final: 0.8102 (tp30) REVERT: A 380 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8524 (mp) REVERT: A 480 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: A 499 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7547 (mtt-85) REVERT: A 503 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8455 (mt) REVERT: A 528 SER cc_start: 0.8381 (m) cc_final: 0.8157 (p) REVERT: A 555 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7457 (tm) outliers start: 21 outliers final: 9 residues processed: 91 average time/residue: 0.4641 time to fit residues: 44.0035 Evaluate side-chains 97 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.0670 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.123287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.101527 restraints weight = 4631.990| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.27 r_work: 0.2877 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.9955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4397 Z= 0.142 Angle : 0.582 8.734 5995 Z= 0.282 Chirality : 0.042 0.274 674 Planarity : 0.004 0.035 726 Dihedral : 4.049 18.879 584 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.31 % Allowed : 23.18 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.36), residues: 536 helix: 2.20 (0.26), residues: 370 sheet: None (None), residues: 0 loop : -0.13 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 560 TYR 0.018 0.002 TYR A 132 PHE 0.025 0.001 PHE A 460 TRP 0.029 0.002 TRP A 534 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 4396) covalent geometry : angle 0.58089 / 0.28 ( 5993) SS BOND : bond 0.00414 / 0.22 ( 1) SS BOND : angle 1.93794 / 1.03 ( 2) hydrogen bonds : bond 0.04469 / 3.13 ( 288) hydrogen bonds : angle 4.41169 / 3.08 ( 843) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.160 Fit side-chains REVERT: A 167 LEU cc_start: 0.8398 (tm) cc_final: 0.8003 (tp) REVERT: A 237 LYS cc_start: 0.5713 (mttt) cc_final: 0.5047 (tppp) REVERT: A 332 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8196 (mt) REVERT: A 351 GLU cc_start: 0.8439 (tp30) cc_final: 0.8169 (tp30) REVERT: A 380 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8554 (mp) REVERT: A 480 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7697 (mp10) REVERT: A 499 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7531 (mtt-85) REVERT: A 503 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8390 (mt) REVERT: A 528 SER cc_start: 0.8366 (m) cc_final: 0.8157 (p) REVERT: A 555 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7472 (tm) outliers start: 15 outliers final: 6 residues processed: 89 average time/residue: 0.4267 time to fit residues: 39.6549 Evaluate side-chains 93 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.123020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.101439 restraints weight = 4618.539| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.25 r_work: 0.2878 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 1.0041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4397 Z= 0.144 Angle : 0.586 8.633 5995 Z= 0.284 Chirality : 0.042 0.290 674 Planarity : 0.004 0.037 726 Dihedral : 4.057 18.907 584 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.19 % Allowed : 22.52 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.36), residues: 536 helix: 2.17 (0.26), residues: 370 sheet: None (None), residues: 0 loop : -0.10 (0.50), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 560 TYR 0.018 0.001 TYR A 132 PHE 0.030 0.001 PHE A 460 TRP 0.028 0.002 TRP A 534 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 4396) covalent geometry : angle 0.58498 / 0.28 ( 5993) SS BOND : bond 0.00346 / 0.18 ( 1) SS BOND : angle 1.87848 / 1.00 ( 2) hydrogen bonds : bond 0.04501 / 3.16 ( 288) hydrogen bonds : angle 4.44947 / 3.11 ( 843) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1589.98 seconds wall clock time: 27 minutes 48.74 seconds (1668.74 seconds total)