Starting phenix.real_space_refine on Sat May 2 10:46:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u7h_63936/05_2026/9u7h_63936.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u7h_63936/05_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_63936/05_2026/9u7h_63936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u7h_63936/05_2026/9u7h_63936.map" model { file = "/net/cci-nas-00/data/ceres_data/9u7h_63936/05_2026/9u7h_63936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u7h_63936/05_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-2.1rc2-6044/lib/python3.9/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, 63 Unusual residues: {' MN': 2, 'GDU': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 0.81, per 1000 atoms: 0.18 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: 0.27 Conformation dependent library (CDL) restraints added in 168.9 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: 0.08 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: 0.35 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 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 2.320 nonbonded pdb=" O2A UDP A 803 " pdb="MN MN A 804 " model vdw 2.188 2.320 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: 1.680 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: 3.710 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 covalent geometry : bond 0.00579 ( 4572) covalent geometry : angle 0.89630 ( 6215) SS BOND : bond 0.37511 ( 1) SS BOND : angle 22.64360 ( 2) hydrogen bonds : bond 0.19478 ( 129) hydrogen bonds : angle 7.17803 ( 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 : 0.111 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 97 average time/residue: 0.0540 time to fit residues: 6.4147 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 : 0.088 ------------------------------------------------------------------------------- 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: 0.6980 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4052 r_free = 0.4052 target = 0.186685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.154948 restraints weight = 5685.814| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.51 r_work: 0.3554 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4573 Z= 0.162 Angle : 0.671 7.784 6217 Z= 0.351 Chirality : 0.045 0.182 668 Planarity : 0.006 0.057 794 Dihedral : 10.516 98.975 693 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.27 % Favored : 91.54 % 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: -2.51 (0.34), residues: 532 helix: -0.60 (0.42), residues: 159 sheet: -1.73 (0.63), residues: 63 loop : -2.32 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 370 TYR 0.009 0.001 TYR A 494 PHE 0.019 0.002 PHE A 529 TRP 0.023 0.002 TRP A 202 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4572) covalent geometry : angle 0.66870 ( 6215) SS BOND : bond 0.01529 ( 1) SS BOND : angle 2.90482 ( 2) hydrogen bonds : bond 0.05935 ( 129) hydrogen bonds : angle 5.28914 ( 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 82 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: A 161 TYR cc_start: 0.8725 (m-80) cc_final: 0.8268 (m-80) REVERT: A 184 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8174 (t0) REVERT: A 221 ARG cc_start: 0.6860 (tpt90) cc_final: 0.6497 (tpt90) REVERT: A 489 GLU cc_start: 0.8091 (tp30) cc_final: 0.7827 (tm-30) REVERT: A 513 GLU cc_start: 0.7908 (mp0) cc_final: 0.6593 (tp30) outliers start: 7 outliers final: 4 residues processed: 78 average time/residue: 0.0513 time to fit residues: 5.0248 Evaluate side-chains 73 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.087 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 41 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS 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 = 0.189584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.158641 restraints weight = 5710.993| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.49 r_work: 0.3571 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1523 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= 0.113 Angle : 0.584 6.222 6217 Z= 0.305 Chirality : 0.042 0.156 668 Planarity : 0.006 0.054 794 Dihedral : 9.071 80.660 690 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.08 % Favored : 91.73 % Rotamer: Outliers : 1.06 % Allowed : 10.17 % Favored : 88.77 % 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: -2.21 (0.35), residues: 532 helix: -0.25 (0.41), residues: 163 sheet: -1.67 (0.62), residues: 63 loop : -2.19 (0.33), residues: 306 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 0.018 0.001 PHE A 529 TRP 0.016 0.001 TRP A 202 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4572) covalent geometry : angle 0.58246 ( 6215) SS BOND : bond 0.01078 ( 1) SS BOND : angle 2.19223 ( 2) hydrogen bonds : bond 0.04391 ( 129) hydrogen bonds : angle 4.85602 ( 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 77 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.108 Fit side-chains REVERT: A 161 TYR cc_start: 0.8641 (m-80) cc_final: 0.8280 (m-80) REVERT: A 360 ARG cc_start: 0.8153 (ttp-170) cc_final: 0.7701 (mtm180) REVERT: A 489 GLU cc_start: 0.7989 (tp30) cc_final: 0.7757 (tm-30) REVERT: A 513 GLU cc_start: 0.7866 (mp0) cc_final: 0.6676 (tp30) outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 0.0511 time to fit residues: 4.7073 Evaluate side-chains 70 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 451 LEU 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: 0.3980 chunk 16 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4084 r_free = 0.4084 target = 0.190204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.156646 restraints weight = 5676.942| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.47 r_work: 0.3583 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: 0.7807 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4573 Z= 0.113 Angle : 0.565 7.033 6217 Z= 0.293 Chirality : 0.042 0.152 668 Planarity : 0.005 0.051 794 Dihedral : 8.645 81.492 690 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.52 % Favored : 92.29 % Rotamer: Outliers : 2.75 % Allowed : 11.65 % Favored : 85.59 % 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: -2.03 (0.35), residues: 532 helix: -0.10 (0.41), residues: 164 sheet: -1.54 (0.64), residues: 63 loop : -2.09 (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 0.016 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 covalent geometry : bond 0.00266 ( 4572) covalent geometry : angle 0.56453 ( 6215) SS BOND : bond 0.00776 ( 1) SS BOND : angle 1.78630 ( 2) hydrogen bonds : bond 0.03998 ( 129) hydrogen bonds : angle 4.67132 ( 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: 13 poor density : 74 time to evaluate : 0.096 Fit side-chains REVERT: A 161 TYR cc_start: 0.8660 (m-80) cc_final: 0.8247 (m-80) REVERT: A 350 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7601 (ptp-170) REVERT: A 360 ARG cc_start: 0.8166 (ttp-170) cc_final: 0.7675 (mtm180) REVERT: A 489 GLU cc_start: 0.7881 (tp30) cc_final: 0.7476 (tm-30) REVERT: A 513 GLU cc_start: 0.7858 (mp0) cc_final: 0.6539 (tp30) outliers start: 13 outliers final: 7 residues processed: 80 average time/residue: 0.0449 time to fit residues: 4.5864 Evaluate side-chains 75 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.091 ------------------------------------------------------------------------------- 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 316 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4042 r_free = 0.4042 target = 0.185175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.154613 restraints weight = 5806.416| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.48 r_work: 0.3535 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1823 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= 0.121 Angle : 0.581 8.715 6217 Z= 0.295 Chirality : 0.042 0.152 668 Planarity : 0.005 0.052 794 Dihedral : 8.511 81.491 690 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.71 % Favored : 92.11 % Rotamer: Outliers : 2.54 % Allowed : 13.98 % Favored : 83.47 % 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: -1.90 (0.35), residues: 532 helix: 0.07 (0.42), residues: 161 sheet: -1.58 (0.64), residues: 64 loop : -2.00 (0.33), residues: 307 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 0.015 0.001 PHE A 529 TRP 0.014 0.001 TRP A 202 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4572) covalent geometry : angle 0.58063 ( 6215) SS BOND : bond 0.00453 ( 1) SS BOND : angle 1.73582 ( 2) hydrogen bonds : bond 0.04087 ( 129) hydrogen bonds : angle 4.67217 ( 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 82 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.168 Fit side-chains REVERT: A 161 TYR cc_start: 0.8592 (m-80) cc_final: 0.8183 (m-80) REVERT: A 233 MET cc_start: 0.8352 (tpp) cc_final: 0.8031 (tpt) REVERT: A 350 ARG cc_start: 0.8013 (mtm110) cc_final: 0.7652 (ptp-170) REVERT: A 360 ARG cc_start: 0.8278 (ttp-170) cc_final: 0.7789 (mtm180) REVERT: A 489 GLU cc_start: 0.7765 (tp30) cc_final: 0.7426 (tm-30) REVERT: A 513 GLU cc_start: 0.7902 (mp0) cc_final: 0.6618 (tp30) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.0455 time to fit residues: 4.3761 Evaluate side-chains 76 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 283 CYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 451 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.184784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153624 restraints weight = 5895.799| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.46 r_work: 0.3515 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4573 Z= 0.146 Angle : 0.607 8.303 6217 Z= 0.309 Chirality : 0.043 0.150 668 Planarity : 0.006 0.052 794 Dihedral : 8.554 80.757 690 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.71 % Favored : 92.11 % Rotamer: Outliers : 2.75 % Allowed : 15.04 % 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: -1.94 (0.35), residues: 532 helix: -0.05 (0.41), residues: 163 sheet: -1.53 (0.66), residues: 64 loop : -1.99 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 360 TYR 0.008 0.001 TYR A 466 PHE 0.017 0.002 PHE A 529 TRP 0.016 0.001 TRP A 202 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4572) covalent geometry : angle 0.60609 ( 6215) SS BOND : bond 0.00704 ( 1) SS BOND : angle 2.09632 ( 2) hydrogen bonds : bond 0.04483 ( 129) hydrogen bonds : angle 4.75503 ( 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 83 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.109 Fit side-chains REVERT: A 161 TYR cc_start: 0.8641 (m-80) cc_final: 0.8188 (m-80) outliers start: 13 outliers final: 11 residues processed: 75 average time/residue: 0.0405 time to fit residues: 3.9749 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 : 0.087 ------------------------------------------------------------------------------- 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 518 MET Chi-restraints excluded: chain A residue 530 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4017 r_free = 0.4017 target = 0.182435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151451 restraints weight = 5844.699| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.49 r_work: 0.3508 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4573 Z= 0.166 Angle : 0.627 8.260 6217 Z= 0.321 Chirality : 0.044 0.148 668 Planarity : 0.006 0.053 794 Dihedral : 8.662 79.977 690 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.46 % Favored : 91.35 % Rotamer: Outliers : 2.33 % Allowed : 15.89 % Favored : 81.78 % 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: -1.97 (0.35), residues: 532 helix: -0.05 (0.41), residues: 160 sheet: -1.03 (0.74), residues: 53 loop : -2.13 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.009 0.001 TYR A 466 PHE 0.017 0.002 PHE A 529 TRP 0.020 0.002 TRP A 202 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 4572) covalent geometry : angle 0.62607 ( 6215) SS BOND : bond 0.00714 ( 1) SS BOND : angle 2.34120 ( 2) hydrogen bonds : bond 0.04841 ( 129) hydrogen bonds : angle 4.86462 ( 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: 11 poor density : 64 time to evaluate : 0.089 Fit side-chains REVERT: A 161 TYR cc_start: 0.8691 (m-80) cc_final: 0.8232 (m-80) REVERT: A 184 ASN cc_start: 0.8526 (t0) cc_final: 0.8183 (t0) outliers start: 11 outliers final: 9 residues processed: 69 average time/residue: 0.0415 time to fit residues: 3.7050 Evaluate side-chains 71 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.0370 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4041 r_free = 0.4041 target = 0.184919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.153617 restraints weight = 5836.208| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.51 r_work: 0.3523 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4573 Z= 0.140 Angle : 0.596 6.767 6217 Z= 0.306 Chirality : 0.043 0.151 668 Planarity : 0.006 0.053 794 Dihedral : 8.513 80.205 690 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.08 % Favored : 91.73 % Rotamer: Outliers : 2.12 % Allowed : 16.74 % Favored : 81.14 % 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: -1.89 (0.35), residues: 532 helix: 0.03 (0.41), residues: 163 sheet: -1.02 (0.75), residues: 53 loop : -2.09 (0.33), residues: 316 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 0.018 0.001 PHE A 529 TRP 0.021 0.001 TRP A 202 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4572) covalent geometry : angle 0.59501 ( 6215) SS BOND : bond 0.00710 ( 1) SS BOND : angle 2.05236 ( 2) hydrogen bonds : bond 0.04462 ( 129) hydrogen bonds : angle 4.77396 ( 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 77 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.089 Fit side-chains REVERT: A 161 TYR cc_start: 0.8566 (m-80) cc_final: 0.8161 (m-80) REVERT: A 184 ASN cc_start: 0.8379 (t0) cc_final: 0.8034 (t0) REVERT: A 350 ARG cc_start: 0.7876 (mtm110) cc_final: 0.7548 (ptp-170) outliers start: 10 outliers final: 10 residues processed: 71 average time/residue: 0.0449 time to fit residues: 4.0544 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 : 0.133 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4007 r_free = 0.4007 target = 0.181518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.150102 restraints weight = 5867.691| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.49 r_work: 0.3474 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4573 Z= 0.212 Angle : 0.682 9.646 6217 Z= 0.350 Chirality : 0.046 0.152 668 Planarity : 0.006 0.055 794 Dihedral : 8.907 79.989 690 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.02 % Favored : 90.79 % Rotamer: Outliers : 2.54 % Allowed : 16.10 % 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: -2.11 (0.35), residues: 532 helix: -0.29 (0.40), residues: 163 sheet: -1.06 (0.76), residues: 53 loop : -2.16 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 53 TYR 0.011 0.002 TYR A 466 PHE 0.019 0.002 PHE A 529 TRP 0.025 0.002 TRP A 202 HIS 0.007 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 4572) covalent geometry : angle 0.68023 ( 6215) SS BOND : bond 0.00715 ( 1) SS BOND : angle 2.61054 ( 2) hydrogen bonds : bond 0.05524 ( 129) hydrogen bonds : angle 5.03548 ( 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 75 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.088 Fit side-chains REVERT: A 161 TYR cc_start: 0.8610 (m-80) cc_final: 0.8107 (m-80) REVERT: A 184 ASN cc_start: 0.8372 (t0) cc_final: 0.8020 (t0) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.0441 time to fit residues: 3.8981 Evaluate side-chains 70 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.087 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 0.0570 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4049 r_free = 0.4049 target = 0.185892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154902 restraints weight = 5820.146| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.49 r_work: 0.3535 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4573 Z= 0.119 Angle : 0.592 9.288 6217 Z= 0.301 Chirality : 0.042 0.147 668 Planarity : 0.006 0.053 794 Dihedral : 8.398 80.974 690 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.65 % Favored : 91.17 % Rotamer: Outliers : 1.27 % Allowed : 17.80 % Favored : 80.93 % 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: -1.74 (0.36), residues: 532 helix: 0.25 (0.41), residues: 162 sheet: -1.05 (0.75), residues: 53 loop : -2.03 (0.33), residues: 317 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 0.018 0.001 PHE A 529 TRP 0.020 0.001 TRP A 202 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4572) covalent geometry : angle 0.59104 ( 6215) SS BOND : bond 0.00712 ( 1) SS BOND : angle 1.86841 ( 2) hydrogen bonds : bond 0.04053 ( 129) hydrogen bonds : angle 4.72978 ( 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 73 residues out of total 472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.087 Fit side-chains REVERT: A 161 TYR cc_start: 0.8522 (m-80) cc_final: 0.8232 (m-80) REVERT: A 184 ASN cc_start: 0.8353 (t0) cc_final: 0.8038 (t0) REVERT: A 233 MET cc_start: 0.7457 (tpt) cc_final: 0.7236 (tpt) REVERT: A 350 ARG cc_start: 0.7884 (mtm110) cc_final: 0.7540 (ptp-170) outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.0447 time to fit residues: 4.0462 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 : 0.087 ------------------------------------------------------------------------------- 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 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4045 r_free = 0.4045 target = 0.185441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.153665 restraints weight = 5850.061| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.41 r_work: 0.3545 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4573 Z= 0.129 Angle : 0.614 10.303 6217 Z= 0.308 Chirality : 0.042 0.152 668 Planarity : 0.006 0.054 794 Dihedral : 8.394 82.181 690 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.46 % Favored : 91.35 % Rotamer: Outliers : 1.27 % Allowed : 17.58 % Favored : 81.14 % 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: -1.67 (0.36), residues: 532 helix: 0.35 (0.42), residues: 163 sheet: -1.02 (0.75), residues: 53 loop : -2.02 (0.33), residues: 316 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 0.018 0.001 PHE A 529 TRP 0.019 0.001 TRP A 202 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4572) covalent geometry : angle 0.61313 ( 6215) SS BOND : bond 0.00682 ( 1) SS BOND : angle 2.00273 ( 2) hydrogen bonds : bond 0.04255 ( 129) hydrogen bonds : angle 4.73691 ( 372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 890.21 seconds wall clock time: 26 minutes 42.13 seconds (1602.13 seconds total)