Starting phenix.real_space_refine on Thu Jul 2 00:13:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7m_61207/07_2026/9j7m_61207.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7m_61207/07_2026/9j7m_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_61207/07_2026/9j7m_61207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7m_61207/07_2026/9j7m_61207.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7m_61207/07_2026/9j7m_61207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7m_61207/07_2026/9j7m_61207.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 221 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'CLR': 3, 'R16': 5, 'TAU': 1, 'Y01': 1} Classifications: {'undetermined': 10, 'water': 15} Link IDs: {None: 23} Chain breaks: 2 Time building chain proxies: 0.96, per 1000 atoms: 0.21 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: 0.28 Conformation dependent library (CDL) restraints added in 164.4 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: 0.12 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: 0.67 Time building geometry restraints manager: 0.35 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 3.210 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 3.210 ... (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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.210 Find NCS groups from input model: 0.020 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:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (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 ARG 0.001 0.000 ARG A 423 TYR 0.012 0.001 TYR A 69 PHE 0.012 0.001 PHE A 474 TRP 0.020 0.001 TRP A 470 HIS 0.004 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.34 ( 4683) covalent geometry : angle 0.81639 / 0.44 ( 6374) SS BOND : bond 0.01038 / 0.69 ( 1) SS BOND : angle 2.33479 / 1.48 ( 2) hydrogen bonds : bond 0.12678 / 7.94 ( 268) hydrogen bonds : angle 4.76216 / 3.52 ( 783) *********************** 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 : 0.141 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: 0.3311 time to fit residues: 21.7254 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 : 0.161 ------------------------------------------------------------------------------- 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 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.5474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.100575 restraints weight = 5104.305| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.71 r_work: 0.2943 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4684 Z= 0.105 Angle : 0.485 6.617 6376 Z= 0.251 Chirality : 0.037 0.158 701 Planarity : 0.004 0.041 746 Dihedral : 9.178 57.992 944 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.36 % Allowed : 16.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.38), residues: 539 helix: 1.83 (0.28), residues: 380 sheet: None (None), residues: 0 loop : -1.55 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.017 0.001 TYR A 69 PHE 0.012 0.001 PHE A 79 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 4683) covalent geometry : angle 0.48155 / 0.25 ( 6374) SS BOND : bond 0.00391 / 0.26 ( 1) SS BOND : angle 3.29072 / 2.35 ( 2) hydrogen bonds : bond 0.04416 / 3.04 ( 268) hydrogen bonds : angle 3.90792 / 2.83 ( 783) *********************** 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 59 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.104 Fit side-chains REVERT: A 69 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7648 (p90) REVERT: A 114 GLU cc_start: 0.7880 (tp30) cc_final: 0.7589 (mm-30) REVERT: A 358 ASP cc_start: 0.7378 (m-30) cc_final: 0.7106 (m-30) REVERT: A 380 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7091 (mtp) outliers start: 11 outliers final: 3 residues processed: 55 average time/residue: 0.4435 time to fit residues: 25.5923 Evaluate side-chains 48 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.0270 chunk 0 optimal weight: 8.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.095422 restraints weight = 5105.467| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.68 r_work: 0.2901 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0943 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= 0.124 Angle : 0.498 5.796 6376 Z= 0.260 Chirality : 0.038 0.145 701 Planarity : 0.004 0.043 746 Dihedral : 8.196 55.972 927 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.00 % Allowed : 16.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.37), residues: 539 helix: 1.99 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.29 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 240 TYR 0.021 0.001 TYR A 69 PHE 0.017 0.002 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 4683) covalent geometry : angle 0.49678 / 0.26 ( 6374) SS BOND : bond 0.00261 / 0.17 ( 1) SS BOND : angle 1.74490 / 1.18 ( 2) hydrogen bonds : bond 0.05179 / 3.58 ( 268) hydrogen bonds : angle 3.95261 / 2.86 ( 783) *********************** 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 60 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.100 Fit side-chains REVERT: A 69 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7631 (p90) REVERT: A 358 ASP cc_start: 0.7387 (m-30) cc_final: 0.7158 (m-30) REVERT: A 380 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7099 (mtp) REVERT: A 395 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7306 (mp) outliers start: 14 outliers final: 8 residues processed: 57 average time/residue: 0.3779 time to fit residues: 22.6360 Evaluate side-chains 56 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 VAL 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 26 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.097173 restraints weight = 5108.032| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.69 r_work: 0.2958 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1009 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= 0.106 Angle : 0.468 5.702 6376 Z= 0.244 Chirality : 0.037 0.137 701 Planarity : 0.004 0.042 746 Dihedral : 7.791 57.638 927 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.15 % Allowed : 18.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.37), residues: 539 helix: 2.08 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -1.24 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.018 0.001 TYR A 69 PHE 0.013 0.001 PHE A 79 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 4683) covalent geometry : angle 0.46767 / 0.24 ( 6374) SS BOND : bond 0.00358 / 0.24 ( 1) SS BOND : angle 1.61201 / 1.04 ( 2) hydrogen bonds : bond 0.04545 / 3.15 ( 268) hydrogen bonds : angle 3.87258 / 2.80 ( 783) *********************** 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 55 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.103 Fit side-chains REVERT: A 69 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7563 (p90) REVERT: A 358 ASP cc_start: 0.7401 (m-30) cc_final: 0.7156 (m-30) REVERT: A 380 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7094 (mtp) outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 0.3877 time to fit residues: 20.8230 Evaluate side-chains 49 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 192 THR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 415 VAL 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 14 optimal weight: 0.0870 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.098607 restraints weight = 5039.932| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.70 r_work: 0.2924 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1046 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= 0.108 Angle : 0.471 5.743 6376 Z= 0.245 Chirality : 0.037 0.137 701 Planarity : 0.004 0.043 746 Dihedral : 7.497 56.214 925 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.36 % Allowed : 17.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.37), residues: 539 helix: 2.12 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.20 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.019 0.001 TYR A 69 PHE 0.014 0.001 PHE A 79 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 4683) covalent geometry : angle 0.47010 / 0.25 ( 6374) SS BOND : bond 0.00368 / 0.25 ( 1) SS BOND : angle 1.55772 / 1.00 ( 2) hydrogen bonds : bond 0.04648 / 3.22 ( 268) hydrogen bonds : angle 3.85058 / 2.79 ( 783) *********************** 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: 11 poor density : 43 time to evaluate : 0.108 Fit side-chains REVERT: A 69 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7830 (p90) REVERT: A 358 ASP cc_start: 0.7493 (m-30) cc_final: 0.7262 (m-30) REVERT: A 380 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7236 (mtp) REVERT: A 395 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7534 (mp) REVERT: A 563 ILE cc_start: 0.6607 (mt) cc_final: 0.6402 (mt) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 0.3741 time to fit residues: 20.5742 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 : 0.098 ------------------------------------------------------------------------------- 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 192 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 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 17 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.096042 restraints weight = 5192.072| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.71 r_work: 0.2920 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1100 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= 0.112 Angle : 0.477 5.801 6376 Z= 0.248 Chirality : 0.037 0.141 701 Planarity : 0.004 0.043 746 Dihedral : 7.452 53.644 925 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.37), residues: 539 helix: 2.11 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.14 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.019 0.001 TYR A 69 PHE 0.014 0.001 PHE A 79 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 4683) covalent geometry : angle 0.47590 / 0.25 ( 6374) SS BOND : bond 0.00379 / 0.25 ( 1) SS BOND : angle 1.66053 / 1.06 ( 2) hydrogen bonds : bond 0.04811 / 3.34 ( 268) hydrogen bonds : angle 3.87366 / 2.80 ( 783) *********************** 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 : 0.105 Fit side-chains REVERT: A 69 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7656 (p90) REVERT: A 358 ASP cc_start: 0.7377 (m-30) cc_final: 0.7147 (m-30) REVERT: A 380 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7053 (mtp) REVERT: A 395 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7308 (mp) REVERT: A 563 ILE cc_start: 0.6306 (mt) cc_final: 0.6091 (mt) outliers start: 13 outliers final: 7 residues processed: 54 average time/residue: 0.3452 time to fit residues: 19.7207 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 : 0.156 ------------------------------------------------------------------------------- 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 415 VAL 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 35 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 13 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.099959 restraints weight = 5085.109| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.71 r_work: 0.2953 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1154 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= 0.098 Angle : 0.452 5.661 6376 Z= 0.235 Chirality : 0.036 0.129 701 Planarity : 0.004 0.042 746 Dihedral : 7.141 57.538 925 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.82 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.37), residues: 539 helix: 2.25 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.07 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.016 0.001 TYR A 69 PHE 0.012 0.001 PHE A 474 TRP 0.017 0.001 TRP A 470 HIS 0.001 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 4683) covalent geometry : angle 0.45153 / 0.23 ( 6374) SS BOND : bond 0.00345 / 0.23 ( 1) SS BOND : angle 1.46731 / 0.91 ( 2) hydrogen bonds : bond 0.04176 / 2.90 ( 268) hydrogen bonds : angle 3.77989 / 2.73 ( 783) *********************** 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 57 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.168 Fit side-chains REVERT: A 69 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7723 (p90) REVERT: A 358 ASP cc_start: 0.7559 (m-30) cc_final: 0.7339 (m-30) REVERT: A 359 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7447 (mt) REVERT: A 380 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7256 (mtp) outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 0.3133 time to fit residues: 18.3023 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 : 0.121 ------------------------------------------------------------------------------- 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 359 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 415 VAL 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 4 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 37 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 48 optimal weight: 0.0870 chunk 13 optimal weight: 7.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.099609 restraints weight = 5162.142| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.71 r_work: 0.2963 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4684 Z= 0.094 Angle : 0.446 5.605 6376 Z= 0.232 Chirality : 0.036 0.123 701 Planarity : 0.004 0.040 746 Dihedral : 6.793 52.594 925 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.37), residues: 539 helix: 2.34 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.08 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.016 0.001 TYR A 69 PHE 0.011 0.001 PHE A 474 TRP 0.018 0.001 TRP A 470 HIS 0.001 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 4683) covalent geometry : angle 0.44533 / 0.23 ( 6374) SS BOND : bond 0.00280 / 0.19 ( 1) SS BOND : angle 1.35648 / 0.85 ( 2) hydrogen bonds : bond 0.03938 / 2.74 ( 268) hydrogen bonds : angle 3.71607 / 2.68 ( 783) *********************** 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 59 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.160 Fit side-chains REVERT: A 69 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7365 (p90) REVERT: A 236 TRP cc_start: 0.6590 (t60) cc_final: 0.6390 (t60) REVERT: A 358 ASP cc_start: 0.7314 (m-30) cc_final: 0.6693 (t0) REVERT: A 359 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7192 (mt) REVERT: A 380 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7051 (mtp) outliers start: 13 outliers final: 7 residues processed: 57 average time/residue: 0.3130 time to fit residues: 18.9805 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 : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER 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 359 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 415 VAL 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 33 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.0070 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.0370 chunk 16 optimal weight: 2.9990 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.095304 restraints weight = 5140.027| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.69 r_work: 0.2940 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1233 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 : 0.472 5.762 6376 Z= 0.246 Chirality : 0.037 0.139 701 Planarity : 0.004 0.042 746 Dihedral : 6.931 55.761 925 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.00 % Allowed : 17.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.37), residues: 539 helix: 2.28 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -1.09 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.020 0.001 TYR A 69 PHE 0.014 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 4683) covalent geometry : angle 0.47169 / 0.25 ( 6374) SS BOND : bond 0.00335 / 0.22 ( 1) SS BOND : angle 1.51698 / 0.97 ( 2) hydrogen bonds : bond 0.04660 / 3.24 ( 268) hydrogen bonds : angle 3.80075 / 2.75 ( 783) *********************** 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 61 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.104 Fit side-chains REVERT: A 69 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7479 (p90) REVERT: A 358 ASP cc_start: 0.7239 (m-30) cc_final: 0.6620 (t0) REVERT: A 359 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7191 (mt) REVERT: A 380 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7025 (mtp) REVERT: A 563 ILE cc_start: 0.6181 (mt) cc_final: 0.5965 (mt) outliers start: 14 outliers final: 9 residues processed: 59 average time/residue: 0.2925 time to fit residues: 18.2329 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 : 0.159 ------------------------------------------------------------------------------- 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 219 ASP Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 415 VAL 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 17 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.094879 restraints weight = 5175.822| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.68 r_work: 0.2929 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4684 Z= 0.115 Angle : 0.483 5.811 6376 Z= 0.252 Chirality : 0.037 0.140 701 Planarity : 0.004 0.042 746 Dihedral : 7.002 59.218 925 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.36 % Allowed : 18.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.37), residues: 539 helix: 2.20 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -1.05 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.020 0.001 TYR A 69 PHE 0.014 0.001 PHE A 79 TRP 0.033 0.001 TRP A 236 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 4683) covalent geometry : angle 0.48201 / 0.25 ( 6374) SS BOND : bond 0.00362 / 0.24 ( 1) SS BOND : angle 1.58368 / 1.02 ( 2) hydrogen bonds : bond 0.04806 / 3.34 ( 268) hydrogen bonds : angle 3.83109 / 2.77 ( 783) ********************** 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 58 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.101 Fit side-chains REVERT: A 69 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7594 (p90) REVERT: A 359 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7318 (mt) REVERT: A 380 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7089 (mtp) REVERT: A 563 ILE cc_start: 0.6331 (mt) cc_final: 0.6128 (mt) outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 0.3285 time to fit residues: 19.8157 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 : 0.159 ------------------------------------------------------------------------------- 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 359 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 415 VAL 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 21 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.097460 restraints weight = 5215.016| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.70 r_work: 0.2953 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1268 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= 0.103 Angle : 0.465 5.709 6376 Z= 0.243 Chirality : 0.037 0.134 701 Planarity : 0.004 0.041 746 Dihedral : 6.815 55.487 925 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.58 % Allowed : 18.03 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.37), residues: 539 helix: 2.29 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -1.05 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.018 0.001 TYR A 69 PHE 0.013 0.001 PHE A 79 TRP 0.032 0.001 TRP A 236 HIS 0.001 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 4683) covalent geometry : angle 0.46428 / 0.24 ( 6374) SS BOND : bond 0.00340 / 0.23 ( 1) SS BOND : angle 1.49612 / 0.94 ( 2) hydrogen bonds : bond 0.04390 / 3.05 ( 268) hydrogen bonds : angle 3.77486 / 2.72 ( 783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1350.69 seconds wall clock time: 23 minutes 43.40 seconds (1423.40 seconds total)