Starting phenix.real_space_refine on Sat May 10 00:44:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8c_61227/05_2025/9j8c_61227.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8c_61227/05_2025/9j8c_61227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j8c_61227/05_2025/9j8c_61227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8c_61227/05_2025/9j8c_61227.map" model { file = "/net/cci-nas-00/data/ceres_data/9j8c_61227/05_2025/9j8c_61227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8c_61227/05_2025/9j8c_61227.cif" } resolution = 2.9 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= 0.057 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 35 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2963 2.51 5 N 677 2.21 5 O 740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 4418 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4311 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 25, 'TRANS': 516} Chain breaks: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 101 Unusual residues: {' CL': 1, ' NA': 2, 'CLR': 3} Classifications: {'undetermined': 6, 'water': 14} Link IDs: {None: 19} Time building chain proxies: 3.09, per 1000 atoms: 0.70 Number of scatterers: 4418 At special positions: 0 Unit cell: (79.9, 69.7, 93.5, 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 35 16.00 Na 2 11.00 O 740 8.00 N 677 7.00 C 2963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " 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: 1.09 Conformation dependent library (CDL) restraints added in 467.7 milliseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 0 sheets defined 76.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.518A pdb=" N PHE A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.819A pdb=" N VAL A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 4.214A pdb=" N TYR A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 83 Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 95 through 111 removed outlier: 3.751A pdb=" N ALA A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.900A pdb=" N TRP A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 119 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 120 " --> pdb=" O VAL A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 115 through 120' Processing helix chain 'A' and resid 121 through 124 Processing helix chain 'A' and resid 125 through 155 removed outlier: 3.973A pdb=" N TYR A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 233 through 253 Processing helix chain 'A' and resid 263 through 283 Proline residue: A 269 - end of helix removed outlier: 4.036A pdb=" N ARG A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.682A pdb=" N GLY A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.907A pdb=" N TRP A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.684A pdb=" N THR A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 372 removed outlier: 3.654A pdb=" N ASP A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 354 " --> pdb=" O CYS A 350 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 370 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 391 - end of helix removed outlier: 3.841A pdb=" N LEU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 435 removed outlier: 3.771A pdb=" N TRP A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 458 Processing helix chain 'A' and resid 459 through 463 removed outlier: 3.907A pdb=" N SER A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.730A pdb=" N TRP A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 498 through 511 removed outlier: 3.601A pdb=" N MET A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 Processing helix chain 'A' and resid 524 through 540 removed outlier: 3.503A pdb=" N VAL A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 568 removed outlier: 4.203A pdb=" N SER A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 579 removed outlier: 3.574A pdb=" N LEU A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 593 removed outlier: 3.521A pdb=" N ALA A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 262 hydrogen bonds defined for protein. 771 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: 1.06 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 963 1.33 - 1.45: 1091 1.45 - 1.57: 2441 1.57 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 4548 Sorted by residual: bond pdb=" C VAL A 261 " pdb=" N VAL A 262 " ideal model delta sigma weight residual 1.334 1.354 -0.020 1.28e-02 6.10e+03 2.50e+00 bond pdb=" C GLY A 177 " pdb=" O GLY A 177 " ideal model delta sigma weight residual 1.233 1.215 0.018 1.18e-02 7.18e+03 2.42e+00 bond pdb=" C VAL A 178 " pdb=" O VAL A 178 " ideal model delta sigma weight residual 1.238 1.219 0.019 1.32e-02 5.74e+03 2.01e+00 bond pdb=" CA VAL A 178 " pdb=" CB VAL A 178 " ideal model delta sigma weight residual 1.540 1.525 0.016 1.15e-02 7.56e+03 1.83e+00 bond pdb=" CA GLY A 80 " pdb=" C GLY A 80 " ideal model delta sigma weight residual 1.513 1.529 -0.016 1.23e-02 6.61e+03 1.68e+00 ... (remaining 4543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 5998 1.48 - 2.97: 160 2.97 - 4.45: 36 4.45 - 5.93: 20 5.93 - 7.41: 4 Bond angle restraints: 6218 Sorted by residual: angle pdb=" N VAL A 262 " pdb=" CA VAL A 262 " pdb=" C VAL A 262 " ideal model delta sigma weight residual 113.16 105.75 7.41 1.49e+00 4.50e-01 2.48e+01 angle pdb=" N GLY A 177 " pdb=" CA GLY A 177 " pdb=" C GLY A 177 " ideal model delta sigma weight residual 110.90 117.72 -6.82 1.53e+00 4.27e-01 1.99e+01 angle pdb=" C LYS A 260 " pdb=" N VAL A 261 " pdb=" CA VAL A 261 " ideal model delta sigma weight residual 121.97 128.80 -6.83 1.80e+00 3.09e-01 1.44e+01 angle pdb=" N ILE A 496 " pdb=" CA ILE A 496 " pdb=" C ILE A 496 " ideal model delta sigma weight residual 111.81 108.90 2.91 8.60e-01 1.35e+00 1.14e+01 angle pdb=" N ALA A 266 " pdb=" CA ALA A 266 " pdb=" C ALA A 266 " ideal model delta sigma weight residual 114.31 110.08 4.23 1.29e+00 6.01e-01 1.08e+01 ... (remaining 6213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 2326 17.05 - 34.11: 282 34.11 - 51.16: 76 51.16 - 68.21: 18 68.21 - 85.27: 3 Dihedral angle restraints: 2705 sinusoidal: 1145 harmonic: 1560 Sorted by residual: dihedral pdb=" CA TRP A 118 " pdb=" C TRP A 118 " pdb=" N ARG A 119 " pdb=" CA ARG A 119 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE A 524 " pdb=" C PHE A 524 " pdb=" N VAL A 525 " pdb=" CA VAL A 525 " ideal model delta harmonic sigma weight residual 180.00 -163.66 -16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA VAL A 434 " pdb=" C VAL A 434 " pdb=" N GLY A 435 " pdb=" CA GLY A 435 " ideal model delta harmonic sigma weight residual 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 621 0.070 - 0.140: 56 0.140 - 0.209: 10 0.209 - 0.279: 4 0.279 - 0.349: 2 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB VAL A 261 " pdb=" CA VAL A 261 " pdb=" CG1 VAL A 261 " pdb=" CG2 VAL A 261 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C14 CLR A 703 " pdb=" C13 CLR A 703 " pdb=" C15 CLR A 703 " pdb=" C8 CLR A 703 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 690 not shown) Planarity restraints: 746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 261 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.51e+00 pdb=" C VAL A 261 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL A 261 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL A 262 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 542 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 543 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 176 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ALA A 176 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA A 176 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 177 " -0.011 2.00e-02 2.50e+03 ... (remaining 743 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1154 2.80 - 3.32: 3949 3.32 - 3.85: 7177 3.85 - 4.37: 8360 4.37 - 4.90: 14815 Nonbonded interactions: 35455 Sorted by model distance: nonbonded pdb=" OD2 ASP A 288 " pdb=" O HOH A 801 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASN A 68 " pdb="NA NA A 706 " model vdw 2.297 2.470 nonbonded pdb=" O ALA A 63 " pdb="NA NA A 706 " model vdw 2.311 2.470 nonbonded pdb=" OG SER A 486 " pdb=" O HOH A 802 " model vdw 2.318 3.040 nonbonded pdb=" N ASP A 599 " pdb=" OD1 ASP A 599 " model vdw 2.340 3.120 ... (remaining 35450 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: 0.850 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.050 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:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4549 Z= 0.156 Angle : 0.671 7.413 6220 Z= 0.364 Chirality : 0.050 0.349 693 Planarity : 0.004 0.047 746 Dihedral : 15.960 85.267 1716 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 23.58 % Favored : 76.42 % 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: 1.43 (0.38), residues: 538 helix: 1.92 (0.29), residues: 369 sheet: None (None), residues: 0 loop : -1.31 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 554 HIS 0.006 0.001 HIS A 370 PHE 0.011 0.001 PHE A 100 TYR 0.015 0.001 TYR A 74 ARG 0.001 0.000 ARG A 500 Details of bonding type rmsd hydrogen bonds : bond 0.17698 ( 262) hydrogen bonds : angle 5.37477 ( 771) SS BOND : bond 0.00048 ( 1) SS BOND : angle 1.11553 ( 2) covalent geometry : bond 0.00297 ( 4548) covalent geometry : angle 0.67053 ( 6218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.474 Fit side-chains REVERT: A 253 ARG cc_start: 0.5691 (ptt180) cc_final: 0.5232 (mtp180) REVERT: A 299 ASP cc_start: 0.8050 (t0) cc_final: 0.7367 (p0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.1777 time to fit residues: 69.9140 Evaluate side-chains 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.3980 chunk 40 optimal weight: 0.0470 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.118158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.091399 restraints weight = 5091.050| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.56 r_work: 0.2737 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4549 Z= 0.119 Angle : 0.503 5.373 6220 Z= 0.261 Chirality : 0.039 0.119 693 Planarity : 0.004 0.038 746 Dihedral : 7.161 59.382 790 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.40 % Allowed : 21.40 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.78 (0.38), residues: 538 helix: 2.10 (0.28), residues: 378 sheet: None (None), residues: 0 loop : -1.14 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 215 HIS 0.005 0.001 HIS A 370 PHE 0.014 0.001 PHE A 84 TYR 0.018 0.001 TYR A 74 ARG 0.001 0.000 ARG A 580 Details of bonding type rmsd hydrogen bonds : bond 0.05664 ( 262) hydrogen bonds : angle 3.99054 ( 771) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.80822 ( 2) covalent geometry : bond 0.00237 ( 4548) covalent geometry : angle 0.50305 ( 6218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.471 Fit side-chains REVERT: A 74 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8341 (p90) REVERT: A 253 ARG cc_start: 0.5704 (ptt180) cc_final: 0.5442 (mtp180) REVERT: A 284 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: A 299 ASP cc_start: 0.8296 (t0) cc_final: 0.7539 (p0) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 1.2460 time to fit residues: 72.5362 Evaluate side-chains 51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 597 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 0.0270 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.117298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.090307 restraints weight = 5092.478| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.60 r_work: 0.2724 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4549 Z= 0.116 Angle : 0.486 5.285 6220 Z= 0.252 Chirality : 0.038 0.117 693 Planarity : 0.004 0.034 746 Dihedral : 7.188 58.450 790 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.40 % Allowed : 21.62 % Favored : 75.98 % 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: 1.94 (0.38), residues: 538 helix: 2.24 (0.28), residues: 379 sheet: None (None), residues: 0 loop : -1.14 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 215 HIS 0.004 0.001 HIS A 370 PHE 0.015 0.001 PHE A 84 TYR 0.018 0.001 TYR A 74 ARG 0.001 0.000 ARG A 580 Details of bonding type rmsd hydrogen bonds : bond 0.05453 ( 262) hydrogen bonds : angle 3.84067 ( 771) SS BOND : bond 0.00208 ( 1) SS BOND : angle 0.83035 ( 2) covalent geometry : bond 0.00240 ( 4548) covalent geometry : angle 0.48628 ( 6218) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.481 Fit side-chains REVERT: A 74 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8350 (p90) REVERT: A 299 ASP cc_start: 0.8164 (t0) cc_final: 0.7501 (p0) REVERT: A 424 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7774 (tp30) outliers start: 11 outliers final: 5 residues processed: 53 average time/residue: 1.3202 time to fit residues: 72.6462 Evaluate side-chains 50 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 0.0030 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 overall best weight: 0.4148 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.120408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.093916 restraints weight = 5137.871| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.55 r_work: 0.2763 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4549 Z= 0.102 Angle : 0.459 5.331 6220 Z= 0.236 Chirality : 0.038 0.127 693 Planarity : 0.004 0.032 746 Dihedral : 7.073 57.110 790 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.40 % Allowed : 22.05 % Favored : 75.55 % 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: 2.15 (0.38), residues: 538 helix: 2.37 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -1.04 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 215 HIS 0.004 0.001 HIS A 370 PHE 0.012 0.001 PHE A 84 TYR 0.014 0.001 TYR A 74 ARG 0.004 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 262) hydrogen bonds : angle 3.70850 ( 771) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.60008 ( 2) covalent geometry : bond 0.00202 ( 4548) covalent geometry : angle 0.45855 ( 6218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.439 Fit side-chains REVERT: A 74 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8125 (p90) REVERT: A 284 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6792 (tm-30) REVERT: A 299 ASP cc_start: 0.8192 (t0) cc_final: 0.7491 (p0) outliers start: 11 outliers final: 5 residues processed: 51 average time/residue: 1.2383 time to fit residues: 65.8128 Evaluate side-chains 49 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 411 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3197 r_free = 0.3197 target = 0.115338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.088210 restraints weight = 5186.003| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.57 r_work: 0.2687 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4549 Z= 0.137 Angle : 0.512 5.486 6220 Z= 0.265 Chirality : 0.039 0.119 693 Planarity : 0.004 0.036 746 Dihedral : 7.317 61.659 790 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.40 % Allowed : 22.27 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.08 (0.38), residues: 538 helix: 2.40 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -1.20 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 215 HIS 0.005 0.001 HIS A 499 PHE 0.019 0.001 PHE A 84 TYR 0.022 0.002 TYR A 74 ARG 0.002 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.05978 ( 262) hydrogen bonds : angle 3.81586 ( 771) SS BOND : bond 0.00916 ( 1) SS BOND : angle 1.33328 ( 2) covalent geometry : bond 0.00314 ( 4548) covalent geometry : angle 0.51133 ( 6218) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.475 Fit side-chains REVERT: A 57 LEU cc_start: 0.6745 (mt) cc_final: 0.6437 (mt) REVERT: A 74 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8456 (p90) REVERT: A 231 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7832 (pt0) REVERT: A 299 ASP cc_start: 0.8198 (t0) cc_final: 0.7498 (p0) REVERT: A 424 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: A 588 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7941 (tp-100) outliers start: 11 outliers final: 5 residues processed: 52 average time/residue: 1.3493 time to fit residues: 72.8808 Evaluate side-chains 53 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 591 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.0020 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.117121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.090029 restraints weight = 5120.885| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.57 r_work: 0.2719 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 : 0.002 0.026 4549 Z= 0.117 Angle : 0.483 5.400 6220 Z= 0.250 Chirality : 0.038 0.117 693 Planarity : 0.004 0.035 746 Dihedral : 7.245 58.480 790 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.40 % Allowed : 22.49 % Favored : 75.11 % 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: 2.15 (0.38), residues: 538 helix: 2.45 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -1.17 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 215 HIS 0.004 0.001 HIS A 370 PHE 0.014 0.001 PHE A 84 TYR 0.019 0.001 TYR A 74 ARG 0.002 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.05366 ( 262) hydrogen bonds : angle 3.75418 ( 771) SS BOND : bond 0.00106 ( 1) SS BOND : angle 0.90535 ( 2) covalent geometry : bond 0.00250 ( 4548) covalent geometry : angle 0.48322 ( 6218) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.433 Fit side-chains REVERT: A 57 LEU cc_start: 0.6711 (mt) cc_final: 0.6435 (mt) REVERT: A 74 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.8314 (p90) REVERT: A 284 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: A 299 ASP cc_start: 0.8205 (t0) cc_final: 0.7518 (p0) REVERT: A 588 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7919 (tp-100) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 1.2746 time to fit residues: 68.9108 Evaluate side-chains 51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 591 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.0470 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.118059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.091001 restraints weight = 5052.500| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.57 r_work: 0.2715 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4549 Z= 0.114 Angle : 0.477 5.390 6220 Z= 0.246 Chirality : 0.038 0.116 693 Planarity : 0.004 0.034 746 Dihedral : 7.217 56.266 790 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.18 % Allowed : 22.27 % Favored : 75.55 % 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: 2.22 (0.38), residues: 538 helix: 2.51 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -1.16 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 215 HIS 0.004 0.001 HIS A 370 PHE 0.014 0.001 PHE A 84 TYR 0.018 0.001 TYR A 74 ARG 0.002 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.05234 ( 262) hydrogen bonds : angle 3.70458 ( 771) SS BOND : bond 0.00290 ( 1) SS BOND : angle 0.87601 ( 2) covalent geometry : bond 0.00242 ( 4548) covalent geometry : angle 0.47683 ( 6218) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.477 Fit side-chains REVERT: A 57 LEU cc_start: 0.6675 (mt) cc_final: 0.6428 (mt) REVERT: A 74 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8359 (p90) REVERT: A 284 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: A 299 ASP cc_start: 0.8201 (t0) cc_final: 0.7509 (p0) REVERT: A 588 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7907 (tp-100) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 1.4089 time to fit residues: 76.0146 Evaluate side-chains 51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 591 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.117874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.090835 restraints weight = 5050.796| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.57 r_work: 0.2711 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4549 Z= 0.119 Angle : 0.483 5.415 6220 Z= 0.250 Chirality : 0.038 0.117 693 Planarity : 0.004 0.035 746 Dihedral : 7.238 57.424 790 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.18 % Allowed : 22.49 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.22 (0.38), residues: 538 helix: 2.51 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -1.17 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 215 HIS 0.004 0.001 HIS A 499 PHE 0.015 0.001 PHE A 84 TYR 0.019 0.001 TYR A 74 ARG 0.002 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.05372 ( 262) hydrogen bonds : angle 3.70885 ( 771) SS BOND : bond 0.00423 ( 1) SS BOND : angle 1.13836 ( 2) covalent geometry : bond 0.00260 ( 4548) covalent geometry : angle 0.48248 ( 6218) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.439 Fit side-chains REVERT: A 57 LEU cc_start: 0.6725 (mt) cc_final: 0.6381 (mt) REVERT: A 74 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8394 (p90) REVERT: A 284 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: A 299 ASP cc_start: 0.8177 (t0) cc_final: 0.7511 (p0) REVERT: A 424 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: A 588 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7931 (tp-100) outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 1.3628 time to fit residues: 70.6436 Evaluate side-chains 51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 591 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 38 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 0.0980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.119786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.092752 restraints weight = 5082.650| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.58 r_work: 0.2738 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4549 Z= 0.106 Angle : 0.465 5.380 6220 Z= 0.239 Chirality : 0.038 0.115 693 Planarity : 0.004 0.034 746 Dihedral : 7.143 55.574 790 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.42 % Favored : 97.40 % Rotamer: Outliers : 2.84 % Allowed : 22.05 % Favored : 75.11 % 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: 2.30 (0.38), residues: 538 helix: 2.54 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -1.10 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 215 HIS 0.004 0.001 HIS A 370 PHE 0.012 0.001 PHE A 84 TYR 0.016 0.001 TYR A 74 ARG 0.002 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 262) hydrogen bonds : angle 3.62984 ( 771) SS BOND : bond 0.00364 ( 1) SS BOND : angle 0.84166 ( 2) covalent geometry : bond 0.00219 ( 4548) covalent geometry : angle 0.46454 ( 6218) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.464 Fit side-chains REVERT: A 57 LEU cc_start: 0.6710 (mt) cc_final: 0.6470 (mt) REVERT: A 74 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8221 (p90) REVERT: A 284 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6930 (tm-30) REVERT: A 299 ASP cc_start: 0.8181 (t0) cc_final: 0.7516 (p0) REVERT: A 588 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7943 (tp-100) outliers start: 13 outliers final: 7 residues processed: 53 average time/residue: 1.3792 time to fit residues: 75.7284 Evaluate side-chains 51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 591 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.117217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.090021 restraints weight = 5027.564| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.56 r_work: 0.2719 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4549 Z= 0.117 Angle : 0.481 5.413 6220 Z= 0.248 Chirality : 0.038 0.116 693 Planarity : 0.004 0.035 746 Dihedral : 7.196 56.575 790 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.79 % Favored : 97.03 % Rotamer: Outliers : 1.75 % Allowed : 23.14 % Favored : 75.11 % 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: 2.29 (0.38), residues: 538 helix: 2.56 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -1.16 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 215 HIS 0.004 0.001 HIS A 370 PHE 0.015 0.001 PHE A 84 TYR 0.019 0.001 TYR A 74 ARG 0.002 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.05242 ( 262) hydrogen bonds : angle 3.67132 ( 771) SS BOND : bond 0.00243 ( 1) SS BOND : angle 1.12977 ( 2) covalent geometry : bond 0.00251 ( 4548) covalent geometry : angle 0.48029 ( 6218) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.425 Fit side-chains REVERT: A 57 LEU cc_start: 0.6716 (mt) cc_final: 0.6422 (mt) REVERT: A 74 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8358 (p90) REVERT: A 284 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: A 299 ASP cc_start: 0.8175 (t0) cc_final: 0.7518 (p0) REVERT: A 588 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7955 (tp-100) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 1.3411 time to fit residues: 70.9958 Evaluate side-chains 51 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TYR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 591 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3218 r_free = 0.3218 target = 0.116793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.089513 restraints weight = 5041.281| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.57 r_work: 0.2702 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4549 Z= 0.123 Angle : 0.490 5.453 6220 Z= 0.254 Chirality : 0.039 0.115 693 Planarity : 0.004 0.035 746 Dihedral : 7.236 58.122 790 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.60 % Favored : 97.21 % Rotamer: Outliers : 1.75 % Allowed : 23.36 % Favored : 74.89 % 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: 2.26 (0.38), residues: 538 helix: 2.56 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.20 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 215 HIS 0.004 0.001 HIS A 370 PHE 0.016 0.001 PHE A 84 TYR 0.020 0.001 TYR A 74 ARG 0.002 0.000 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.05526 ( 262) hydrogen bonds : angle 3.70222 ( 771) SS BOND : bond 0.00259 ( 1) SS BOND : angle 1.15903 ( 2) covalent geometry : bond 0.00271 ( 4548) covalent geometry : angle 0.48970 ( 6218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.28 seconds wall clock time: 55 minutes 24.05 seconds (3324.05 seconds total)