Starting phenix.real_space_refine on Thu Jun 5 00:00:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7m_61207/06_2025/9j7m_61207.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7m_61207/06_2025/9j7m_61207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j7m_61207/06_2025/9j7m_61207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7m_61207/06_2025/9j7m_61207.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7m_61207/06_2025/9j7m_61207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7m_61207/06_2025/9j7m_61207.cif" } resolution = 2.82 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= -0.001 sd= 0.070 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 33 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3093 2.51 5 N 664 2.21 5 O 760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 4552 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4329 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 28, 'TRANS': 514} Chain breaks: 1 Chain: "A" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 223 Unusual residues: {' CL': 1, ' NA': 1, 'CLR': 3, 'R16': 5, 'TAU': 1, 'Y01': 1} Classifications: {'undetermined': 12, 'water': 15} Link IDs: {None: 26} Time building chain proxies: 3.59, per 1000 atoms: 0.79 Number of scatterers: 4552 At special positions: 0 Unit cell: (73.1, 64.6, 95.2, 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 33 16.00 Na 1 11.00 O 760 8.00 N 664 7.00 C 3093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.04 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: 1.40 Conformation dependent library (CDL) restraints added in 538.3 milliseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 990 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 75.7% alpha, 0.4% 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 46 through 59 removed outlier: 3.599A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.620A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.980A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 121 through 138 removed outlier: 4.313A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 251 through 266 removed outlier: 3.716A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.671A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.019A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 removed outlier: 3.610A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 356 removed outlier: 3.573A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 4.133A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 416 removed outlier: 3.565A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 removed outlier: 3.522A pdb=" N PHE A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 4.266A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.568A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.729A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.406A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 removed outlier: 3.652A pdb=" N LEU A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 268 hydrogen bonds defined for protein. 783 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: 1.10 Time building geometry restraints manager: 1.41 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: 899 1.33 - 1.45: 1170 1.45 - 1.57: 2564 1.57 - 1.69: 3 1.69 - 1.81: 47 Bond restraints: 4683 Sorted by residual: bond pdb=" N ILE A 235 " pdb=" CA ILE A 235 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.06e-02 8.90e+03 1.54e+01 bond pdb=" CAY Y01 A 710 " pdb=" OAW Y01 A 710 " ideal model delta sigma weight residual 1.332 1.394 -0.062 2.00e-02 2.50e+03 9.59e+00 bond pdb=" CAI Y01 A 710 " pdb=" CAZ Y01 A 710 " ideal model delta sigma weight residual 1.332 1.394 -0.062 2.00e-02 2.50e+03 9.52e+00 bond pdb=" N HIS A 161 " pdb=" CA HIS A 161 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.33e-02 5.65e+03 9.29e+00 bond pdb=" N THR A 168 " pdb=" CA THR A 168 " ideal model delta sigma weight residual 1.452 1.485 -0.033 1.11e-02 8.12e+03 8.97e+00 ... (remaining 4678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 6258 2.70 - 5.40: 102 5.40 - 8.10: 11 8.10 - 10.80: 1 10.80 - 13.50: 2 Bond angle restraints: 6374 Sorted by residual: angle pdb=" CAM Y01 A 710 " pdb=" CAY Y01 A 710 " pdb=" OAW Y01 A 710 " ideal model delta sigma weight residual 111.19 124.69 -13.50 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C CYS A 162 " pdb=" CA CYS A 162 " pdb=" CB CYS A 162 " ideal model delta sigma weight residual 111.46 103.92 7.54 1.71e+00 3.42e-01 1.94e+01 angle pdb=" O2 TAU A 701 " pdb=" S TAU A 701 " pdb=" O3 TAU A 701 " ideal model delta sigma weight residual 113.11 101.14 11.97 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N PRO A 585 " pdb=" CA PRO A 585 " pdb=" C PRO A 585 " ideal model delta sigma weight residual 110.95 104.73 6.22 1.62e+00 3.81e-01 1.47e+01 angle pdb=" N ILE A 235 " pdb=" CA ILE A 235 " pdb=" C ILE A 235 " ideal model delta sigma weight residual 112.12 108.90 3.22 8.40e-01 1.42e+00 1.47e+01 ... (remaining 6369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 2472 17.17 - 34.35: 285 34.35 - 51.52: 90 51.52 - 68.69: 18 68.69 - 85.87: 3 Dihedral angle restraints: 2868 sinusoidal: 1304 harmonic: 1564 Sorted by residual: dihedral pdb=" CG ARG A 177 " pdb=" CD ARG A 177 " pdb=" NE ARG A 177 " pdb=" CZ ARG A 177 " ideal model delta sinusoidal sigma weight residual 90.00 133.75 -43.75 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CB LYS A 73 " pdb=" CG LYS A 73 " pdb=" CD LYS A 73 " pdb=" CE LYS A 73 " ideal model delta sinusoidal sigma weight residual 60.00 118.33 -58.33 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA LYS A 577 " pdb=" CB LYS A 577 " pdb=" CG LYS A 577 " pdb=" CD LYS A 577 " ideal model delta sinusoidal sigma weight residual -60.00 -117.38 57.38 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 2865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 589 0.064 - 0.129: 80 0.129 - 0.193: 26 0.193 - 0.257: 4 0.257 - 0.322: 2 Chirality restraints: 701 Sorted by residual: chirality pdb=" CBH Y01 A 710 " pdb=" CAT Y01 A 710 " pdb=" CAZ Y01 A 710 " pdb=" CBF Y01 A 710 " both_signs ideal model delta sigma weight residual False -2.85 -2.53 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CBF Y01 A 710 " pdb=" CAS Y01 A 710 " pdb=" CBD Y01 A 710 " pdb=" CBH Y01 A 710 " both_signs ideal model delta sigma weight residual False -2.45 -2.73 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C14 CLR A 707 " pdb=" C13 CLR A 707 " pdb=" C15 CLR A 707 " pdb=" C8 CLR A 707 " both_signs ideal model delta sigma weight residual False -2.32 -2.57 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 698 not shown) Planarity restraints: 746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 423 " 0.259 9.50e-02 1.11e+02 1.16e-01 8.26e+00 pdb=" NE ARG A 423 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 423 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 423 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 423 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 427 " 0.227 9.50e-02 1.11e+02 1.02e-01 6.38e+00 pdb=" NE ARG A 427 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 427 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 427 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 427 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 577 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C LYS A 577 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS A 577 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR A 578 " 0.012 2.00e-02 2.50e+03 ... (remaining 743 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 391 2.74 - 3.28: 4246 3.28 - 3.82: 7407 3.82 - 4.36: 8607 4.36 - 4.90: 15665 Nonbonded interactions: 36316 Sorted by model distance: nonbonded pdb=" OH TYR A 489 " pdb=" O GLY A 501 " model vdw 2.205 3.040 nonbonded pdb=" ND2 ASN A 63 " pdb=" OD1 ASN A 333 " model vdw 2.335 3.120 nonbonded pdb=" O VAL A 59 " pdb="NA NA A 711 " model vdw 2.337 2.470 nonbonded pdb=" O SER A 365 " pdb=" OG SER A 365 " model vdw 2.348 3.040 nonbonded pdb="NA NA A 711 " pdb=" O HOH A 808 " model vdw 2.368 2.470 ... (remaining 36311 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: 1.490 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.020 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 0.062 4684 Z= 0.341 Angle : 0.817 13.502 6376 Z= 0.445 Chirality : 0.055 0.322 701 Planarity : 0.008 0.116 746 Dihedral : 15.915 85.866 1875 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.43 % Allowed : 17.38 % Favored : 79.18 % 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: 1.19 (0.38), residues: 539 helix: 1.79 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -1.58 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 470 HIS 0.004 0.001 HIS A 164 PHE 0.012 0.001 PHE A 474 TYR 0.012 0.001 TYR A 69 ARG 0.001 0.000 ARG A 423 Details of bonding type rmsd hydrogen bonds : bond 0.12678 ( 268) hydrogen bonds : angle 4.76216 ( 783) SS BOND : bond 0.01038 ( 1) SS BOND : angle 2.33479 ( 2) covalent geometry : bond 0.00552 ( 4683) covalent geometry : angle 0.81639 ( 6374) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.444 Fit side-chains REVERT: A 442 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8140 (tt) outliers start: 16 outliers final: 14 residues processed: 62 average time/residue: 0.7947 time to fit residues: 52.1275 Evaluate side-chains 62 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 573 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.128999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.098369 restraints weight = 4991.322| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.70 r_work: 0.2928 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4684 Z= 0.116 Angle : 0.502 6.724 6376 Z= 0.261 Chirality : 0.038 0.158 701 Planarity : 0.004 0.042 746 Dihedral : 9.285 57.890 944 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.79 % Allowed : 16.31 % Favored : 80.90 % 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: 1.35 (0.38), residues: 539 helix: 1.87 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -1.42 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 PHE 0.014 0.001 PHE A 79 TYR 0.019 0.001 TYR A 69 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04909 ( 268) hydrogen bonds : angle 3.97637 ( 783) SS BOND : bond 0.00276 ( 1) SS BOND : angle 3.54966 ( 2) covalent geometry : bond 0.00258 ( 4683) covalent geometry : angle 0.49793 ( 6374) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.459 Fit side-chains REVERT: A 69 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7685 (p90) REVERT: A 358 ASP cc_start: 0.7379 (m-30) cc_final: 0.7105 (m-30) REVERT: A 380 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7093 (mtp) REVERT: A 395 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7234 (mp) outliers start: 13 outliers final: 4 residues processed: 58 average time/residue: 0.9194 time to fit residues: 56.1847 Evaluate side-chains 51 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 16 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.125922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.095226 restraints weight = 5039.475| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.74 r_work: 0.2876 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4684 Z= 0.140 Angle : 0.523 5.882 6376 Z= 0.274 Chirality : 0.039 0.157 701 Planarity : 0.005 0.046 746 Dihedral : 8.574 53.907 928 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.22 % Allowed : 17.17 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.37), residues: 539 helix: 1.89 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.39 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.003 0.002 HIS A 161 PHE 0.017 0.002 PHE A 79 TYR 0.023 0.001 TYR A 69 ARG 0.001 0.000 ARG A 240 Details of bonding type rmsd hydrogen bonds : bond 0.05703 ( 268) hydrogen bonds : angle 4.03985 ( 783) SS BOND : bond 0.00270 ( 1) SS BOND : angle 1.97676 ( 2) covalent geometry : bond 0.00330 ( 4683) covalent geometry : angle 0.52192 ( 6374) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.537 Fit side-chains REVERT: A 69 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.8151 (p90) REVERT: A 358 ASP cc_start: 0.7677 (m-30) cc_final: 0.7426 (m-30) REVERT: A 380 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7402 (mtp) REVERT: A 395 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7888 (mp) outliers start: 15 outliers final: 8 residues processed: 58 average time/residue: 0.7951 time to fit residues: 49.0875 Evaluate side-chains 55 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.128374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.097885 restraints weight = 5076.225| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.70 r_work: 0.2922 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4684 Z= 0.109 Angle : 0.475 5.700 6376 Z= 0.248 Chirality : 0.037 0.141 701 Planarity : 0.004 0.043 746 Dihedral : 8.345 58.234 927 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.58 % Allowed : 17.60 % Favored : 79.83 % 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: 1.54 (0.37), residues: 539 helix: 2.03 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.29 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 PHE 0.013 0.001 PHE A 474 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04698 ( 268) hydrogen bonds : angle 3.91678 ( 783) SS BOND : bond 0.00374 ( 1) SS BOND : angle 1.70867 ( 2) covalent geometry : bond 0.00242 ( 4683) covalent geometry : angle 0.47403 ( 6374) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.443 Fit side-chains REVERT: A 69 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7575 (p90) REVERT: A 358 ASP cc_start: 0.7347 (m-30) cc_final: 0.7087 (m-30) REVERT: A 380 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7071 (mtp) outliers start: 12 outliers final: 5 residues processed: 53 average time/residue: 0.9137 time to fit residues: 51.1686 Evaluate side-chains 52 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 0.0170 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.126833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.096184 restraints weight = 5188.077| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.69 r_work: 0.2922 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4684 Z= 0.110 Angle : 0.473 5.734 6376 Z= 0.247 Chirality : 0.037 0.140 701 Planarity : 0.004 0.043 746 Dihedral : 8.171 57.401 926 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.15 % Allowed : 17.60 % Favored : 80.26 % 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: 1.64 (0.37), residues: 539 helix: 2.09 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.19 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 PHE 0.014 0.001 PHE A 79 TYR 0.019 0.001 TYR A 69 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 268) hydrogen bonds : angle 3.87909 ( 783) SS BOND : bond 0.00375 ( 1) SS BOND : angle 1.61511 ( 2) covalent geometry : bond 0.00246 ( 4683) covalent geometry : angle 0.47233 ( 6374) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.510 Fit side-chains REVERT: A 69 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7624 (p90) REVERT: A 358 ASP cc_start: 0.7328 (m-30) cc_final: 0.7101 (m-30) REVERT: A 380 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7022 (mtp) REVERT: A 395 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7213 (mp) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.8600 time to fit residues: 47.4872 Evaluate side-chains 50 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.128139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.098005 restraints weight = 5079.517| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.64 r_work: 0.2909 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4684 Z= 0.113 Angle : 0.475 5.774 6376 Z= 0.248 Chirality : 0.037 0.142 701 Planarity : 0.004 0.044 746 Dihedral : 7.671 51.454 925 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.79 % Allowed : 17.38 % Favored : 79.83 % 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: 1.67 (0.37), residues: 539 helix: 2.10 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.14 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 PHE 0.014 0.001 PHE A 79 TYR 0.019 0.001 TYR A 69 ARG 0.001 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 268) hydrogen bonds : angle 3.88059 ( 783) SS BOND : bond 0.00390 ( 1) SS BOND : angle 1.67283 ( 2) covalent geometry : bond 0.00255 ( 4683) covalent geometry : angle 0.47399 ( 6374) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.499 Fit side-chains REVERT: A 69 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7460 (p90) REVERT: A 358 ASP cc_start: 0.7291 (m-30) cc_final: 0.7075 (m-30) REVERT: A 380 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6999 (mtp) REVERT: A 395 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7133 (mp) outliers start: 13 outliers final: 6 residues processed: 53 average time/residue: 0.8142 time to fit residues: 45.9487 Evaluate side-chains 54 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.096923 restraints weight = 5072.472| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.68 r_work: 0.2940 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4684 Z= 0.105 Angle : 0.463 5.703 6376 Z= 0.242 Chirality : 0.037 0.137 701 Planarity : 0.004 0.043 746 Dihedral : 7.464 55.445 925 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.15 % Allowed : 18.03 % Favored : 79.83 % 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 (0.37), residues: 539 helix: 2.16 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.06 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 PHE 0.013 0.001 PHE A 79 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 268) hydrogen bonds : angle 3.84403 ( 783) SS BOND : bond 0.00355 ( 1) SS BOND : angle 1.54355 ( 2) covalent geometry : bond 0.00234 ( 4683) covalent geometry : angle 0.46223 ( 6374) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.465 Fit side-chains REVERT: A 69 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7596 (p90) REVERT: A 358 ASP cc_start: 0.7397 (m-30) cc_final: 0.7181 (m-30) REVERT: A 359 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7302 (mt) REVERT: A 380 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7086 (mtp) REVERT: A 395 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7267 (mp) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.8322 time to fit residues: 45.9722 Evaluate side-chains 52 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0000 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.128394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.097925 restraints weight = 5135.963| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.69 r_work: 0.2986 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4684 Z= 0.099 Angle : 0.452 5.660 6376 Z= 0.236 Chirality : 0.036 0.131 701 Planarity : 0.004 0.042 746 Dihedral : 7.303 55.058 925 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.58 % Allowed : 17.60 % Favored : 79.83 % 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: 1.92 (0.37), residues: 539 helix: 2.26 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.97 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.001 0.001 HIS A 212 PHE 0.012 0.001 PHE A 474 TYR 0.017 0.001 TYR A 69 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 268) hydrogen bonds : angle 3.77925 ( 783) SS BOND : bond 0.00314 ( 1) SS BOND : angle 1.48057 ( 2) covalent geometry : bond 0.00217 ( 4683) covalent geometry : angle 0.45179 ( 6374) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.536 Fit side-chains REVERT: A 69 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7508 (p90) REVERT: A 236 TRP cc_start: 0.6646 (t60) cc_final: 0.6435 (t60) REVERT: A 358 ASP cc_start: 0.7405 (m-30) cc_final: 0.7176 (m-30) REVERT: A 359 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7268 (mt) REVERT: A 380 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7063 (mtp) outliers start: 12 outliers final: 5 residues processed: 54 average time/residue: 0.8349 time to fit residues: 47.9446 Evaluate side-chains 52 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.125966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.095384 restraints weight = 5100.683| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.68 r_work: 0.2917 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4684 Z= 0.118 Angle : 0.485 5.839 6376 Z= 0.254 Chirality : 0.038 0.147 701 Planarity : 0.004 0.043 746 Dihedral : 7.534 59.220 925 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.36 % Allowed : 17.81 % Favored : 79.83 % 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: 1.79 (0.37), residues: 539 helix: 2.16 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.99 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 PHE 0.016 0.001 PHE A 79 TYR 0.021 0.001 TYR A 69 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.05017 ( 268) hydrogen bonds : angle 3.87564 ( 783) SS BOND : bond 0.00372 ( 1) SS BOND : angle 1.66099 ( 2) covalent geometry : bond 0.00271 ( 4683) covalent geometry : angle 0.48395 ( 6374) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.515 Fit side-chains REVERT: A 69 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7599 (p90) REVERT: A 236 TRP cc_start: 0.6678 (t60) cc_final: 0.6441 (t60) REVERT: A 359 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7284 (mt) REVERT: A 380 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7081 (mtp) outliers start: 11 outliers final: 7 residues processed: 54 average time/residue: 0.9194 time to fit residues: 52.4635 Evaluate side-chains 56 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 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 = 0.3411 r_free = 0.3411 target = 0.126195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.095634 restraints weight = 5087.703| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.67 r_work: 0.2944 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4684 Z= 0.105 Angle : 0.465 5.715 6376 Z= 0.243 Chirality : 0.037 0.136 701 Planarity : 0.004 0.042 746 Dihedral : 7.360 56.273 925 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.15 % Allowed : 17.81 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.37), residues: 539 helix: 2.22 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.96 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.001 0.001 HIS A 164 PHE 0.013 0.001 PHE A 79 TYR 0.018 0.001 TYR A 69 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 268) hydrogen bonds : angle 3.81972 ( 783) SS BOND : bond 0.00338 ( 1) SS BOND : angle 1.53288 ( 2) covalent geometry : bond 0.00232 ( 4683) covalent geometry : angle 0.46460 ( 6374) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.459 Fit side-chains REVERT: A 69 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7478 (p90) REVERT: A 236 TRP cc_start: 0.6637 (t60) cc_final: 0.6425 (t60) REVERT: A 359 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7237 (mt) REVERT: A 380 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7003 (mtp) outliers start: 10 outliers final: 6 residues processed: 51 average time/residue: 0.9478 time to fit residues: 51.0561 Evaluate side-chains 53 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.125196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.094743 restraints weight = 5059.606| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.67 r_work: 0.2904 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4684 Z= 0.129 Angle : 0.501 5.902 6376 Z= 0.262 Chirality : 0.039 0.151 701 Planarity : 0.004 0.043 746 Dihedral : 7.368 53.272 925 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.36 % Allowed : 17.60 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.37), residues: 539 helix: 2.10 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -1.02 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 PHE 0.016 0.002 PHE A 79 TYR 0.022 0.001 TYR A 69 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.05289 ( 268) hydrogen bonds : angle 3.91664 ( 783) SS BOND : bond 0.00411 ( 1) SS BOND : angle 1.73375 ( 2) covalent geometry : bond 0.00303 ( 4683) covalent geometry : angle 0.49978 ( 6374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3105.24 seconds wall clock time: 53 minutes 50.38 seconds (3230.38 seconds total)