Starting phenix.real_space_refine on Thu Jul 2 00:19:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u7h_63936/07_2026/9u7h_63936.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u7h_63936/07_2026/9u7h_63936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u7h_63936/07_2026/9u7h_63936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u7h_63936/07_2026/9u7h_63936.map" model { file = "/net/cci-nas-00/data/ceres_data/9u7h_63936/07_2026/9u7h_63936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u7h_63936/07_2026/9u7h_63936.cif" } resolution = 3.08 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= -0.000 sd= 0.003 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 Mn 2 7.51 5 P 4 5.49 5 S 25 5.16 5 C 2825 2.51 5 N 778 2.21 5 O 820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 4454 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4363 Classifications: {'peptide': 534} Link IDs: {'PCIS': 3, 'PTRANS': 31, 'TRANS': 499} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LYZ:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'GDU': 1, 'UDP': 1} Classifications: {'undetermined': 2} Chain breaks: 2 Time building chain proxies: 0.96, per 1000 atoms: 0.22 Number of scatterers: 4454 At special positions: 0 Unit cell: (101.745, 75.24, 70.965, 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) Mn 2 24.99 S 25 16.00 P 4 15.00 O 820 8.00 N 778 7.00 C 2825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 283 " distance=2.41 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: 0.35 Conformation dependent library (CDL) restraints added in 115.1 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 5 sheets defined 32.5% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.805A pdb=" N GLY A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.785A pdb=" N ARG A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.801A pdb=" N TYR A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.657A pdb=" N ALA A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.517A pdb=" N LYS A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 276 removed outlier: 3.815A pdb=" N PHE A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 319 removed outlier: 3.578A pdb=" N GLU A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 316 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 365 removed outlier: 3.527A pdb=" N MET A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 removed outlier: 3.689A pdb=" N GLN A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 427 removed outlier: 3.825A pdb=" N GLY A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.670A pdb=" N LYS A 508 " --> pdb=" O GLN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 520 through 529 Proline residue: A 526 - end of helix removed outlier: 3.678A pdb=" N PHE A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.934A pdb=" N SER A 114 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 59 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 187 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N CYS A 283 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA A 189 " --> pdb=" O CYS A 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 202 removed outlier: 3.706A pdb=" N TRP A 202 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 233 " --> pdb=" O TRP A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 372 removed outlier: 7.932A pdb=" N VAL A 372 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET A 345 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 342 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 346 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR A 494 " --> pdb=" O ARG A 471 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ARG A 471 " --> pdb=" O TYR A 494 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N THR A 496 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ARG A 469 " --> pdb=" O THR A 496 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA A 498 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLY A 468 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 438 through 439 129 hydrogen bonds defined for protein. 372 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: 0.65 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1458 1.35 - 1.48: 1166 1.48 - 1.61: 1903 1.61 - 1.73: 1 1.73 - 1.86: 44 Bond restraints: 4572 Sorted by residual: bond pdb=" C4 GDU A 801 " pdb=" N3 GDU A 801 " ideal model delta sigma weight residual 1.388 1.333 0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" C4 GDU A 801 " pdb=" C5 GDU A 801 " ideal model delta sigma weight residual 1.440 1.389 0.051 2.00e-02 2.50e+03 6.39e+00 bond pdb=" C5 GDU A 801 " pdb=" C6 GDU A 801 " ideal model delta sigma weight residual 1.343 1.388 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" O3A GDU A 801 " pdb=" PA GDU A 801 " ideal model delta sigma weight residual 1.647 1.603 0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" C2 GDU A 801 " pdb=" O2 GDU A 801 " ideal model delta sigma weight residual 1.211 1.250 -0.039 2.00e-02 2.50e+03 3.76e+00 ... (remaining 4567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 6000 2.21 - 4.43: 192 4.43 - 6.64: 17 6.64 - 8.85: 4 8.85 - 11.06: 2 Bond angle restraints: 6215 Sorted by residual: angle pdb=" CA ILE A 218 " pdb=" C ILE A 218 " pdb=" N PRO A 219 " ideal model delta sigma weight residual 120.83 116.66 4.17 6.10e-01 2.69e+00 4.67e+01 angle pdb=" N SER A 110 " pdb=" CA SER A 110 " pdb=" C SER A 110 " ideal model delta sigma weight residual 114.75 108.74 6.01 1.26e+00 6.30e-01 2.27e+01 angle pdb=" C ILE A 218 " pdb=" CA ILE A 218 " pdb=" CB ILE A 218 " ideal model delta sigma weight residual 114.00 109.06 4.94 1.31e+00 5.83e-01 1.42e+01 angle pdb=" CB MET A 380 " pdb=" CG MET A 380 " pdb=" SD MET A 380 " ideal model delta sigma weight residual 112.70 123.76 -11.06 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O ILE A 218 " pdb=" C ILE A 218 " pdb=" N PRO A 219 " ideal model delta sigma weight residual 120.42 122.76 -2.34 6.40e-01 2.44e+00 1.34e+01 ... (remaining 6210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 2489 17.81 - 35.61: 256 35.61 - 53.42: 53 53.42 - 71.23: 13 71.23 - 89.03: 6 Dihedral angle restraints: 2817 sinusoidal: 1222 harmonic: 1595 Sorted by residual: dihedral pdb=" CA TYR A 400 " pdb=" C TYR A 400 " pdb=" N HIS A 401 " pdb=" CA HIS A 401 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA GLU A 183 " pdb=" C GLU A 183 " pdb=" N ASN A 184 " pdb=" CA ASN A 184 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA LEU A 58 " pdb=" C LEU A 58 " pdb=" N LEU A 59 " pdb=" CA LEU A 59 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 2814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 460 0.046 - 0.092: 168 0.092 - 0.137: 36 0.137 - 0.183: 2 0.183 - 0.229: 2 Chirality restraints: 668 Sorted by residual: chirality pdb=" C1D GDU A 801 " pdb=" C2D GDU A 801 " pdb=" N1 GDU A 801 " pdb=" O4D GDU A 801 " both_signs ideal model delta sigma weight residual False 2.21 2.43 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C2' GDU A 801 " pdb=" C1' GDU A 801 " pdb=" C3' GDU A 801 " pdb=" O2' GDU A 801 " both_signs ideal model delta sigma weight residual False -2.28 -2.49 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN A 381 " pdb=" N ASN A 381 " pdb=" C ASN A 381 " pdb=" CB ASN A 381 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 665 not shown) Planarity restraints: 794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 67 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO A 68 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 146 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C LEU A 146 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A 146 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 147 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 118 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 119 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " -0.025 5.00e-02 4.00e+02 ... (remaining 791 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 18 2.38 - 3.01: 2371 3.01 - 3.64: 6204 3.64 - 4.27: 9429 4.27 - 4.90: 15867 Nonbonded interactions: 33889 Sorted by model distance: nonbonded pdb=" O2B UDP A 803 " pdb="MN MN A 804 " model vdw 1.750 3.060 nonbonded pdb=" O2A UDP A 803 " pdb="MN MN A 804 " model vdw 2.188 3.060 nonbonded pdb=" OH TYR A 492 " pdb=" OH TYR A 494 " model vdw 2.237 3.040 nonbonded pdb=" O ASN A 96 " pdb=" OG1 THR A 99 " model vdw 2.274 3.040 nonbonded pdb=" OE1 GLU A 314 " pdb=" NH2 ARG A 439 " model vdw 2.280 3.120 ... (remaining 33884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.140 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.540 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.008 0.375 4573 Z= 0.385 Angle : 0.984 26.683 6217 Z= 0.544 Chirality : 0.049 0.229 668 Planarity : 0.006 0.064 794 Dihedral : 15.291 89.031 1778 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.28 % Favored : 88.53 % Rotamer: Outliers : 0.64 % Allowed : 0.85 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.33), residues: 532 helix: -0.88 (0.40), residues: 162 sheet: -1.39 (0.71), residues: 53 loop : -2.60 (0.30), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 370 TYR 0.010 0.002 TYR A 567 PHE 0.026 0.002 PHE A 440 TRP 0.026 0.003 TRP A 202 HIS 0.007 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.27 ( 4572) covalent geometry : angle 0.89630 / 0.51 ( 6215) SS BOND : bond 0.37511 / 19.74 ( 1) SS BOND : angle 22.64360 / 12.36 ( 2) hydrogen bonds : bond 0.19478 / 13.61 ( 129) hydrogen bonds : angle 7.17803 / 4.88 ( 372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.167 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 97 average time/residue: 0.0842 time to fit residues: 10.0377 Evaluate side-chains 75 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 HIS A 352 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.188029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154278 restraints weight = 5644.536| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.48 r_work: 0.3558 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4573 Z= 0.150 Angle : 0.656 7.550 6217 Z= 0.342 Chirality : 0.045 0.194 668 Planarity : 0.006 0.056 794 Dihedral : 10.556 101.708 693 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.71 % Favored : 92.11 % Rotamer: Outliers : 1.48 % Allowed : 8.26 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.34), residues: 532 helix: -0.63 (0.41), residues: 163 sheet: -1.74 (0.63), residues: 63 loop : -2.27 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 370 TYR 0.008 0.001 TYR A 417 PHE 0.018 0.002 PHE A 529 TRP 0.021 0.002 TRP A 202 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 4572) covalent geometry : angle 0.65262 / 0.34 ( 6215) SS BOND : bond 0.00955 / 0.50 ( 1) SS BOND : angle 3.56169 / 1.88 ( 2) hydrogen bonds : bond 0.05501 / 3.91 ( 129) hydrogen bonds : angle 5.21291 / 3.45 ( 372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 161 TYR cc_start: 0.8680 (m-80) cc_final: 0.8249 (m-80) REVERT: A 184 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8197 (t0) REVERT: A 489 GLU cc_start: 0.8043 (tp30) cc_final: 0.7806 (tm-30) REVERT: A 513 GLU cc_start: 0.7857 (mp0) cc_final: 0.6641 (tp30) outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 0.0886 time to fit residues: 8.5306 Evaluate side-chains 75 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 518 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.188511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.154676 restraints weight = 5641.688| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.50 r_work: 0.3549 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4573 Z= 0.132 Angle : 0.604 6.544 6217 Z= 0.315 Chirality : 0.043 0.155 668 Planarity : 0.006 0.055 794 Dihedral : 9.237 82.658 690 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.46 % Favored : 91.35 % Rotamer: Outliers : 1.48 % Allowed : 10.38 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.34), residues: 532 helix: -0.34 (0.41), residues: 160 sheet: -1.64 (0.63), residues: 63 loop : -2.21 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 370 TYR 0.008 0.001 TYR A 417 PHE 0.018 0.001 PHE A 529 TRP 0.018 0.001 TRP A 202 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 4572) covalent geometry : angle 0.60236 / 0.31 ( 6215) SS BOND : bond 0.01056 / 0.56 ( 1) SS BOND : angle 2.35404 / 1.26 ( 2) hydrogen bonds : bond 0.04743 / 3.38 ( 129) hydrogen bonds : angle 4.92897 / 3.25 ( 372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.136 Fit side-chains REVERT: A 161 TYR cc_start: 0.8570 (m-80) cc_final: 0.8149 (m-80) REVERT: A 360 ARG cc_start: 0.8036 (ttp-170) cc_final: 0.7561 (mtm180) REVERT: A 489 GLU cc_start: 0.7824 (tp30) cc_final: 0.7601 (tm-30) REVERT: A 513 GLU cc_start: 0.7851 (mp0) cc_final: 0.6637 (tp30) outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 0.0763 time to fit residues: 6.9974 Evaluate side-chains 72 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.188660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.154974 restraints weight = 5620.748| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.45 r_work: 0.3565 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4573 Z= 0.130 Angle : 0.591 6.824 6217 Z= 0.306 Chirality : 0.043 0.152 668 Planarity : 0.006 0.055 794 Dihedral : 8.861 81.001 690 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.08 % Favored : 91.73 % Rotamer: Outliers : 3.18 % Allowed : 12.08 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.35), residues: 532 helix: -0.30 (0.41), residues: 164 sheet: -1.48 (0.64), residues: 63 loop : -2.10 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.008 0.001 TYR A 417 PHE 0.017 0.001 PHE A 529 TRP 0.018 0.001 TRP A 202 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 4572) covalent geometry : angle 0.59031 / 0.31 ( 6215) SS BOND : bond 0.00769 / 0.40 ( 1) SS BOND : angle 1.95659 / 1.07 ( 2) hydrogen bonds : bond 0.04442 / 3.18 ( 129) hydrogen bonds : angle 4.81260 / 3.18 ( 372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.158 Fit side-chains REVERT: A 161 TYR cc_start: 0.8699 (m-80) cc_final: 0.8221 (m-80) REVERT: A 350 ARG cc_start: 0.8069 (mtm110) cc_final: 0.7566 (ptp-170) REVERT: A 360 ARG cc_start: 0.8182 (ttp-170) cc_final: 0.7703 (mtm180) REVERT: A 489 GLU cc_start: 0.7992 (tp30) cc_final: 0.7773 (tm-30) REVERT: A 513 GLU cc_start: 0.7843 (mp0) cc_final: 0.6598 (tp30) outliers start: 15 outliers final: 11 residues processed: 78 average time/residue: 0.0738 time to fit residues: 7.2238 Evaluate side-chains 81 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 518 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.185056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.152813 restraints weight = 5710.033| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.42 r_work: 0.3552 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4573 Z= 0.123 Angle : 0.596 9.019 6217 Z= 0.300 Chirality : 0.042 0.153 668 Planarity : 0.005 0.053 794 Dihedral : 8.590 79.668 690 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.08 % Favored : 91.73 % Rotamer: Outliers : 2.75 % Allowed : 13.98 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.95 (0.35), residues: 532 helix: -0.03 (0.42), residues: 161 sheet: -1.46 (0.65), residues: 63 loop : -2.03 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 370 TYR 0.008 0.001 TYR A 417 PHE 0.016 0.001 PHE A 529 TRP 0.015 0.001 TRP A 202 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 4572) covalent geometry : angle 0.59498 / 0.30 ( 6215) SS BOND : bond 0.00743 / 0.39 ( 1) SS BOND : angle 1.92914 / 1.04 ( 2) hydrogen bonds : bond 0.04224 / 3.03 ( 129) hydrogen bonds : angle 4.73045 / 3.13 ( 372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.119 Fit side-chains REVERT: A 161 TYR cc_start: 0.8486 (m-80) cc_final: 0.8083 (m-80) REVERT: A 184 ASN cc_start: 0.8458 (t0) cc_final: 0.8133 (t0) REVERT: A 350 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7570 (ptp-170) REVERT: A 360 ARG cc_start: 0.8146 (ttp-170) cc_final: 0.7650 (mtm180) REVERT: A 513 GLU cc_start: 0.7865 (mp0) cc_final: 0.6631 (tp30) outliers start: 13 outliers final: 11 residues processed: 76 average time/residue: 0.0699 time to fit residues: 6.6265 Evaluate side-chains 78 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 518 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.187536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.155117 restraints weight = 5809.753| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.47 r_work: 0.3564 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4573 Z= 0.111 Angle : 0.573 8.201 6217 Z= 0.290 Chirality : 0.042 0.152 668 Planarity : 0.005 0.053 794 Dihedral : 8.301 78.807 690 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.33 % Favored : 92.48 % Rotamer: Outliers : 2.33 % Allowed : 15.04 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.84 (0.35), residues: 532 helix: 0.18 (0.42), residues: 161 sheet: -1.53 (0.65), residues: 64 loop : -2.01 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.008 0.001 TYR A 417 PHE 0.015 0.001 PHE A 529 TRP 0.014 0.001 TRP A 202 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 4572) covalent geometry : angle 0.57193 / 0.29 ( 6215) SS BOND : bond 0.00725 / 0.38 ( 1) SS BOND : angle 1.85686 / 1.00 ( 2) hydrogen bonds : bond 0.03853 / 2.76 ( 129) hydrogen bonds : angle 4.64383 / 3.06 ( 372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.164 Fit side-chains REVERT: A 161 TYR cc_start: 0.8472 (m-80) cc_final: 0.8098 (m-80) REVERT: A 184 ASN cc_start: 0.8456 (t0) cc_final: 0.8101 (t0) REVERT: A 233 MET cc_start: 0.7569 (tpt) cc_final: 0.7298 (tpt) REVERT: A 350 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7634 (ptp-170) REVERT: A 360 ARG cc_start: 0.8140 (ttp-170) cc_final: 0.7637 (mtm180) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.0663 time to fit residues: 5.9857 Evaluate side-chains 75 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 518 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.185231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.153830 restraints weight = 5791.759| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.45 r_work: 0.3540 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4573 Z= 0.141 Angle : 0.593 6.891 6217 Z= 0.303 Chirality : 0.043 0.151 668 Planarity : 0.006 0.055 794 Dihedral : 8.411 78.158 690 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.46 % Favored : 91.35 % Rotamer: Outliers : 2.12 % Allowed : 15.68 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.84 (0.35), residues: 532 helix: 0.09 (0.41), residues: 164 sheet: -1.48 (0.66), residues: 64 loop : -1.98 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 351 TYR 0.008 0.001 TYR A 466 PHE 0.017 0.001 PHE A 529 TRP 0.017 0.001 TRP A 202 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 4572) covalent geometry : angle 0.59166 / 0.30 ( 6215) SS BOND : bond 0.00681 / 0.36 ( 1) SS BOND : angle 2.15230 / 1.18 ( 2) hydrogen bonds : bond 0.04490 / 3.18 ( 129) hydrogen bonds : angle 4.74953 / 3.14 ( 372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.166 Fit side-chains REVERT: A 161 TYR cc_start: 0.8515 (m-80) cc_final: 0.8058 (m-80) REVERT: A 184 ASN cc_start: 0.8423 (t0) cc_final: 0.8064 (t0) REVERT: A 350 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7614 (ptp-170) outliers start: 10 outliers final: 10 residues processed: 69 average time/residue: 0.0667 time to fit residues: 5.8326 Evaluate side-chains 73 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 530 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 0.0470 chunk 16 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.189081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.156649 restraints weight = 5801.163| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.45 r_work: 0.3582 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4573 Z= 0.100 Angle : 0.563 9.492 6217 Z= 0.283 Chirality : 0.041 0.148 668 Planarity : 0.005 0.048 794 Dihedral : 7.957 76.861 690 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.52 % Favored : 92.29 % Rotamer: Outliers : 1.91 % Allowed : 15.89 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.50 (0.36), residues: 532 helix: 0.57 (0.43), residues: 163 sheet: -1.38 (0.66), residues: 63 loop : -1.87 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.007 0.001 TYR A 417 PHE 0.015 0.001 PHE A 529 TRP 0.015 0.001 TRP A 202 HIS 0.003 0.000 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 4572) covalent geometry : angle 0.56219 / 0.28 ( 6215) SS BOND : bond 0.00740 / 0.39 ( 1) SS BOND : angle 1.71497 / 0.91 ( 2) hydrogen bonds : bond 0.03414 / 2.45 ( 129) hydrogen bonds : angle 4.51471 / 2.99 ( 372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.178 Fit side-chains REVERT: A 161 TYR cc_start: 0.8413 (m-80) cc_final: 0.8149 (m-80) REVERT: A 184 ASN cc_start: 0.8363 (t0) cc_final: 0.8067 (t0) REVERT: A 350 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7625 (ptp-170) REVERT: A 360 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7609 (mtm180) REVERT: A 518 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7244 (mmp) outliers start: 9 outliers final: 4 residues processed: 73 average time/residue: 0.0736 time to fit residues: 6.7875 Evaluate side-chains 71 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 518 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.0060 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.188459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.157739 restraints weight = 5812.450| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.47 r_work: 0.3565 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4573 Z= 0.111 Angle : 0.561 6.236 6217 Z= 0.285 Chirality : 0.041 0.150 668 Planarity : 0.005 0.050 794 Dihedral : 7.966 77.413 690 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.71 % Favored : 92.11 % Rotamer: Outliers : 1.27 % Allowed : 17.37 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.46 (0.36), residues: 532 helix: 0.60 (0.42), residues: 163 sheet: -1.46 (0.66), residues: 64 loop : -1.81 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.007 0.001 TYR A 417 PHE 0.015 0.001 PHE A 529 TRP 0.015 0.001 TRP A 202 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 4572) covalent geometry : angle 0.56034 / 0.28 ( 6215) SS BOND : bond 0.00743 / 0.39 ( 1) SS BOND : angle 1.91873 / 1.02 ( 2) hydrogen bonds : bond 0.03712 / 2.65 ( 129) hydrogen bonds : angle 4.56193 / 3.01 ( 372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.100 Fit side-chains REVERT: A 161 TYR cc_start: 0.8604 (m-80) cc_final: 0.8213 (m-80) REVERT: A 184 ASN cc_start: 0.8469 (t0) cc_final: 0.8150 (t0) REVERT: A 350 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7635 (ptp-170) REVERT: A 360 ARG cc_start: 0.8297 (ttp-170) cc_final: 0.7753 (mtm180) REVERT: A 518 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7381 (mmp) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.0759 time to fit residues: 6.6090 Evaluate side-chains 71 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 518 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 0.0670 chunk 41 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.189056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.158385 restraints weight = 5779.610| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.50 r_work: 0.3571 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4573 Z= 0.109 Angle : 0.563 8.017 6217 Z= 0.284 Chirality : 0.041 0.148 668 Planarity : 0.005 0.051 794 Dihedral : 7.873 77.585 690 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.08 % Favored : 91.73 % Rotamer: Outliers : 1.06 % Allowed : 17.58 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.37 (0.36), residues: 532 helix: 0.72 (0.43), residues: 163 sheet: -1.44 (0.67), residues: 64 loop : -1.77 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.007 0.001 TYR A 417 PHE 0.014 0.001 PHE A 529 TRP 0.015 0.001 TRP A 202 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 4572) covalent geometry : angle 0.56220 / 0.28 ( 6215) SS BOND : bond 0.00887 / 0.47 ( 1) SS BOND : angle 2.02629 / 1.07 ( 2) hydrogen bonds : bond 0.03534 / 2.54 ( 129) hydrogen bonds : angle 4.51569 / 2.99 ( 372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.195 Fit side-chains REVERT: A 161 TYR cc_start: 0.8447 (m-80) cc_final: 0.8115 (m-80) REVERT: A 184 ASN cc_start: 0.8317 (t0) cc_final: 0.8052 (t0) REVERT: A 280 MET cc_start: 0.7109 (mtm) cc_final: 0.6820 (mtp) REVERT: A 350 ARG cc_start: 0.7900 (mtm110) cc_final: 0.7584 (ptp-170) REVERT: A 360 ARG cc_start: 0.8173 (ttp-170) cc_final: 0.7607 (mtm180) REVERT: A 518 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7690 (mmp) outliers start: 5 outliers final: 4 residues processed: 70 average time/residue: 0.0889 time to fit residues: 7.7421 Evaluate side-chains 69 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 518 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.0370 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.187687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.156643 restraints weight = 5784.727| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.40 r_work: 0.3584 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4573 Z= 0.111 Angle : 0.564 6.257 6217 Z= 0.287 Chirality : 0.041 0.151 668 Planarity : 0.005 0.051 794 Dihedral : 7.872 78.096 690 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.71 % Favored : 92.11 % Rotamer: Outliers : 1.27 % Allowed : 17.37 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % 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: -1.31 (0.37), residues: 532 helix: 0.77 (0.43), residues: 163 sheet: -1.49 (0.66), residues: 64 loop : -1.71 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.007 0.001 TYR A 466 PHE 0.015 0.001 PHE A 529 TRP 0.015 0.001 TRP A 202 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 4572) covalent geometry : angle 0.56293 / 0.29 ( 6215) SS BOND : bond 0.00778 / 0.41 ( 1) SS BOND : angle 2.00093 / 1.06 ( 2) hydrogen bonds : bond 0.03637 / 2.60 ( 129) hydrogen bonds : angle 4.51189 / 2.99 ( 372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1255.57 seconds wall clock time: 22 minutes 9.35 seconds (1329.35 seconds total)