Starting phenix.real_space_refine on Thu Jul 2 10:46:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvf_42618/07_2026/8uvf_42618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvf_42618/07_2026/8uvf_42618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uvf_42618/07_2026/8uvf_42618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvf_42618/07_2026/8uvf_42618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uvf_42618/07_2026/8uvf_42618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvf_42618/07_2026/8uvf_42618.map" } resolution = 2.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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 P 4 5.49 5 S 52 5.16 5 Na 4 4.78 5 C 5818 2.51 5 N 1272 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 8520 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4011 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 34, 'TRANS': 478} Chain breaks: 2 Chain: "A" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 247 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'3PE': 2, 'C14': 3, 'CLR': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Restraints were copied for chains: B Time building chain proxies: 3.51, per 1000 atoms: 0.41 Number of scatterers: 8520 At special positions: 0 Unit cell: (84.975, 110.55, 82.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 4 15.00 Na 4 11.00 O 1370 8.00 N 1272 7.00 C 5818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.93 Conformation dependent library (CDL) restraints added in 293.3 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 84.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 removed outlier: 3.614A pdb=" N ALA A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 34 Proline residue: A 24 - end of helix Proline residue: A 29 - end of helix removed outlier: 3.884A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 54 Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.751A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.676A pdb=" N PHE A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.613A pdb=" N GLY A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 143 through 163 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 220 through 247 removed outlier: 3.656A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.834A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.989A pdb=" N LEU A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 301 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 320 through 335 Processing helix chain 'A' and resid 339 through 359 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 377 through 390 removed outlier: 3.796A pdb=" N ILE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.907A pdb=" N PHE A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 426 through 446 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 483 through 503 Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 505 through 517 removed outlier: 3.833A pdb=" N LEU A 509 " --> pdb=" O HIS A 505 " (cutoff:3.500A) Proline residue: A 512 - end of helix Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 540 through 566 removed outlier: 4.198A pdb=" N LEU A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 14 through 34 Proline residue: B 24 - end of helix Proline residue: B 29 - end of helix removed outlier: 3.883A pdb=" N PHE B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 54 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.750A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 87 through 106 removed outlier: 3.676A pdb=" N PHE B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.614A pdb=" N GLY B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 143 through 163 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 220 through 247 removed outlier: 3.656A pdb=" N ILE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.835A pdb=" N THR B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 267 removed outlier: 3.988A pdb=" N LEU B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 301 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 320 through 335 Processing helix chain 'B' and resid 339 through 359 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 377 through 390 removed outlier: 3.796A pdb=" N ILE B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.907A pdb=" N PHE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 426 through 446 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 457 through 460 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 483 through 503 Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 505 through 517 removed outlier: 3.833A pdb=" N LEU B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Proline residue: B 512 - end of helix Processing helix chain 'B' and resid 527 through 535 Processing helix chain 'B' and resid 540 through 566 removed outlier: 4.198A pdb=" N LEU B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 572 Processing helix chain 'B' and resid 577 through 581 556 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1208 1.30 - 1.43: 2184 1.43 - 1.55: 5264 1.55 - 1.68: 16 1.68 - 1.81: 90 Bond restraints: 8762 Sorted by residual: bond pdb=" C PRO A 83 " pdb=" O PRO A 83 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.32e-02 5.74e+03 2.14e+01 bond pdb=" C PRO B 83 " pdb=" O PRO B 83 " ideal model delta sigma weight residual 1.237 1.177 0.061 1.32e-02 5.74e+03 2.12e+01 bond pdb=" C GLN A 84 " pdb=" O GLN A 84 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.28e-02 6.10e+03 1.28e+01 bond pdb=" C GLN B 84 " pdb=" O GLN B 84 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.28e-02 6.10e+03 1.25e+01 bond pdb=" C PHE A 86 " pdb=" O PHE A 86 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.41e-02 5.03e+03 1.06e+01 ... (remaining 8757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 11373 1.38 - 2.76: 403 2.76 - 4.13: 93 4.13 - 5.51: 39 5.51 - 6.89: 12 Bond angle restraints: 11920 Sorted by residual: angle pdb=" CA LEU B 87 " pdb=" C LEU B 87 " pdb=" O LEU B 87 " ideal model delta sigma weight residual 121.87 114.98 6.89 1.10e+00 8.26e-01 3.92e+01 angle pdb=" CA LEU A 87 " pdb=" C LEU A 87 " pdb=" O LEU A 87 " ideal model delta sigma weight residual 121.87 114.99 6.88 1.10e+00 8.26e-01 3.92e+01 angle pdb=" CA LEU A 87 " pdb=" C LEU A 87 " pdb=" N ASP A 88 " ideal model delta sigma weight residual 115.30 121.99 -6.69 1.33e+00 5.65e-01 2.53e+01 angle pdb=" CA LEU B 87 " pdb=" C LEU B 87 " pdb=" N ASP B 88 " ideal model delta sigma weight residual 115.30 121.97 -6.67 1.33e+00 5.65e-01 2.51e+01 angle pdb=" O CYS A 82 " pdb=" C CYS A 82 " pdb=" N PRO A 83 " ideal model delta sigma weight residual 120.71 117.45 3.26 9.40e-01 1.13e+00 1.20e+01 ... (remaining 11915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 5350 24.85 - 49.71: 162 49.71 - 74.56: 37 74.56 - 99.41: 25 99.41 - 124.27: 8 Dihedral angle restraints: 5582 sinusoidal: 2624 harmonic: 2958 Sorted by residual: dihedral pdb=" C PHE B 86 " pdb=" N PHE B 86 " pdb=" CA PHE B 86 " pdb=" CB PHE B 86 " ideal model delta harmonic sigma weight residual -122.60 -135.99 13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" C PHE A 86 " pdb=" N PHE A 86 " pdb=" CA PHE A 86 " pdb=" CB PHE A 86 " ideal model delta harmonic sigma weight residual -122.60 -135.98 13.38 0 2.50e+00 1.60e-01 2.86e+01 dihedral pdb=" N PHE B 86 " pdb=" C PHE B 86 " pdb=" CA PHE B 86 " pdb=" CB PHE B 86 " ideal model delta harmonic sigma weight residual 122.80 134.36 -11.56 0 2.50e+00 1.60e-01 2.14e+01 ... (remaining 5579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1323 0.098 - 0.195: 61 0.195 - 0.293: 2 0.293 - 0.390: 2 0.390 - 0.488: 2 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA PHE B 86 " pdb=" N PHE B 86 " pdb=" C PHE B 86 " pdb=" CB PHE B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CA PHE A 86 " pdb=" N PHE A 86 " pdb=" C PHE A 86 " pdb=" CB PHE A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA LEU B 87 " pdb=" N LEU B 87 " pdb=" C LEU B 87 " pdb=" CB LEU B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1387 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 82 " -0.011 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C CYS B 82 " 0.035 2.00e-02 2.50e+03 pdb=" O CYS B 82 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO B 83 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 82 " 0.011 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C CYS A 82 " -0.035 2.00e-02 2.50e+03 pdb=" O CYS A 82 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 83 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 527 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO B 528 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 528 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 528 " 0.023 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 605 2.74 - 3.28: 8786 3.28 - 3.82: 15290 3.82 - 4.36: 18000 4.36 - 4.90: 31043 Nonbonded interactions: 73724 Sorted by model distance: nonbonded pdb=" O LEU B 561 " pdb=" OG1 THR B 565 " model vdw 2.198 3.040 nonbonded pdb=" O LEU A 561 " pdb=" OG1 THR A 565 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASN B 484 " pdb="NA NA B 702 " model vdw 2.289 3.210 nonbonded pdb=" OD1 ASN A 484 " pdb="NA NA A 702 " model vdw 2.290 3.210 nonbonded pdb=" NZ LYS A 10 " pdb=" O TRP B 401 " model vdw 2.293 3.120 ... (remaining 73719 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.100 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.870 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 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 : 0.005 0.061 8762 Z= 0.256 Angle : 0.675 6.889 11920 Z= 0.357 Chirality : 0.049 0.488 1390 Planarity : 0.006 0.057 1384 Dihedral : 15.064 124.265 3658 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.47 % Allowed : 0.70 % Favored : 98.84 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.27), residues: 1014 helix: 1.77 (0.19), residues: 784 sheet: None (None), residues: 0 loop : 0.52 (0.45), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 228 TYR 0.017 0.002 TYR B 85 PHE 0.028 0.002 PHE A 363 TRP 0.020 0.001 TRP B 418 HIS 0.008 0.002 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.26 ( 8762) covalent geometry : angle 0.67533 / 0.36 (11920) hydrogen bonds : bond 0.12006 / 7.95 ( 556) hydrogen bonds : angle 4.64040 / 3.58 ( 1626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.337 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 144 average time/residue: 0.6826 time to fit residues: 103.9337 Evaluate side-chains 119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain B residue 86 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0370 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 457 HIS B 538 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.115828 restraints weight = 7829.407| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.38 r_work: 0.3285 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8762 Z= 0.136 Angle : 0.608 8.472 11920 Z= 0.295 Chirality : 0.042 0.139 1390 Planarity : 0.005 0.046 1384 Dihedral : 11.439 88.945 1836 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.58 % Allowed : 5.35 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.27), residues: 1014 helix: 1.83 (0.18), residues: 788 sheet: None (None), residues: 0 loop : 0.46 (0.47), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 15 TYR 0.010 0.001 TYR B 226 PHE 0.020 0.001 PHE B 363 TRP 0.020 0.002 TRP A 418 HIS 0.011 0.003 HIS B 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8762) covalent geometry : angle 0.60801 / 0.29 (11920) hydrogen bonds : bond 0.04019 / 2.72 ( 556) hydrogen bonds : angle 4.02132 / 3.15 ( 1626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: B 123 GLN cc_start: 0.7918 (mp10) cc_final: 0.7705 (mp-120) REVERT: B 151 MET cc_start: 0.8719 (mmm) cc_final: 0.8336 (mmm) outliers start: 5 outliers final: 2 residues processed: 126 average time/residue: 0.5752 time to fit residues: 77.3867 Evaluate side-chains 119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain B residue 86 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 457 HIS A 538 HIS B 457 HIS B 538 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.154354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.114877 restraints weight = 7799.678| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.40 r_work: 0.3274 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8762 Z= 0.125 Angle : 0.550 6.923 11920 Z= 0.274 Chirality : 0.041 0.149 1390 Planarity : 0.005 0.047 1384 Dihedral : 10.103 89.009 1836 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.70 % Allowed : 7.67 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.27), residues: 1014 helix: 1.90 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.33 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 227 TYR 0.006 0.001 TYR B 332 PHE 0.017 0.001 PHE A 352 TRP 0.022 0.002 TRP A 418 HIS 0.015 0.004 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 8762) covalent geometry : angle 0.54998 / 0.27 (11920) hydrogen bonds : bond 0.03838 / 2.60 ( 556) hydrogen bonds : angle 3.97608 / 3.12 ( 1626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 231 TRP cc_start: 0.8409 (m100) cc_final: 0.8175 (t-100) REVERT: B 86 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.7671 (t80) REVERT: B 123 GLN cc_start: 0.7927 (mp10) cc_final: 0.7651 (mp-120) REVERT: B 151 MET cc_start: 0.8717 (mmm) cc_final: 0.8274 (mmm) REVERT: B 445 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7210 (mp0) outliers start: 6 outliers final: 2 residues processed: 123 average time/residue: 0.5129 time to fit residues: 67.7878 Evaluate side-chains 118 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 445 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 457 HIS A 538 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.151676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111820 restraints weight = 7913.454| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.42 r_work: 0.3230 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8762 Z= 0.155 Angle : 0.586 7.295 11920 Z= 0.292 Chirality : 0.043 0.160 1390 Planarity : 0.005 0.046 1384 Dihedral : 10.404 88.277 1836 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.28 % Allowed : 8.37 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.27), residues: 1014 helix: 1.85 (0.18), residues: 794 sheet: None (None), residues: 0 loop : 0.39 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 227 TYR 0.008 0.001 TYR B 332 PHE 0.019 0.002 PHE A 352 TRP 0.025 0.002 TRP A 418 HIS 0.014 0.003 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8762) covalent geometry : angle 0.58620 / 0.29 (11920) hydrogen bonds : bond 0.04194 / 2.81 ( 556) hydrogen bonds : angle 4.08204 / 3.18 ( 1626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8110 (mp10) cc_final: 0.7869 (mp-120) REVERT: B 86 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.7576 (t80) REVERT: B 123 GLN cc_start: 0.8021 (mp10) cc_final: 0.7767 (mp-120) REVERT: B 151 MET cc_start: 0.8691 (mmm) cc_final: 0.8171 (mmm) REVERT: B 439 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8193 (mtp) REVERT: B 445 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: B 546 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7952 (ptt-90) outliers start: 11 outliers final: 5 residues processed: 120 average time/residue: 0.4564 time to fit residues: 58.6765 Evaluate side-chains 120 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 546 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 457 HIS B 457 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.152233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112558 restraints weight = 7929.272| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.42 r_work: 0.3240 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8762 Z= 0.132 Angle : 0.552 7.120 11920 Z= 0.276 Chirality : 0.042 0.172 1390 Planarity : 0.005 0.048 1384 Dihedral : 10.407 89.299 1836 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.74 % Allowed : 8.49 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.27), residues: 1014 helix: 1.92 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.32 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 227 TYR 0.006 0.001 TYR B 332 PHE 0.018 0.001 PHE A 352 TRP 0.024 0.002 TRP A 418 HIS 0.018 0.003 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8762) covalent geometry : angle 0.55220 / 0.28 (11920) hydrogen bonds : bond 0.03857 / 2.60 ( 556) hydrogen bonds : angle 3.98890 / 3.12 ( 1626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7159 (t80) REVERT: A 123 GLN cc_start: 0.8069 (mp10) cc_final: 0.7822 (mp-120) REVERT: A 413 GLU cc_start: 0.7619 (mm-30) cc_final: 0.6461 (tm-30) REVERT: B 86 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.7468 (t80) REVERT: B 123 GLN cc_start: 0.8014 (mp10) cc_final: 0.7741 (mp-120) REVERT: B 151 MET cc_start: 0.8686 (mmm) cc_final: 0.8219 (mmm) REVERT: B 439 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8163 (mtp) REVERT: B 543 ASP cc_start: 0.8080 (m-30) cc_final: 0.7863 (m-30) REVERT: B 546 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7879 (ptt-90) outliers start: 15 outliers final: 4 residues processed: 124 average time/residue: 0.4628 time to fit residues: 61.3971 Evaluate side-chains 118 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 546 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 ASN A 457 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.151508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111792 restraints weight = 7871.847| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.41 r_work: 0.3232 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8762 Z= 0.140 Angle : 0.568 7.336 11920 Z= 0.283 Chirality : 0.042 0.182 1390 Planarity : 0.006 0.052 1384 Dihedral : 10.500 89.716 1836 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.63 % Allowed : 9.53 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.27), residues: 1014 helix: 1.89 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.36 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 227 TYR 0.006 0.001 TYR B 332 PHE 0.019 0.002 PHE A 352 TRP 0.025 0.002 TRP A 418 HIS 0.021 0.003 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8762) covalent geometry : angle 0.56808 / 0.28 (11920) hydrogen bonds : bond 0.04027 / 2.72 ( 556) hydrogen bonds : angle 4.03556 / 3.15 ( 1626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7067 (t80) REVERT: A 123 GLN cc_start: 0.8057 (mp10) cc_final: 0.7823 (mp-120) REVERT: A 338 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7265 (mt) REVERT: A 413 GLU cc_start: 0.7743 (mm-30) cc_final: 0.6629 (tm-30) REVERT: A 445 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: B 86 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7505 (t80) REVERT: B 123 GLN cc_start: 0.7963 (mp10) cc_final: 0.7688 (mp-120) REVERT: B 151 MET cc_start: 0.8669 (mmm) cc_final: 0.8199 (mmm) REVERT: B 227 ARG cc_start: 0.7110 (mtp-110) cc_final: 0.6710 (ttp-110) REVERT: B 385 ILE cc_start: 0.8599 (mm) cc_final: 0.8387 (mt) REVERT: B 439 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8227 (mtp) outliers start: 14 outliers final: 6 residues processed: 122 average time/residue: 0.4269 time to fit residues: 56.0287 Evaluate side-chains 123 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 ASN A 457 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.148126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107972 restraints weight = 7981.274| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.40 r_work: 0.3169 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8762 Z= 0.132 Angle : 0.551 7.153 11920 Z= 0.275 Chirality : 0.042 0.191 1390 Planarity : 0.005 0.051 1384 Dihedral : 10.336 89.737 1836 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.63 % Allowed : 9.77 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.27), residues: 1014 helix: 1.92 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.35 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 227 TYR 0.006 0.001 TYR B 332 PHE 0.018 0.001 PHE A 352 TRP 0.024 0.002 TRP A 418 HIS 0.017 0.003 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8762) covalent geometry : angle 0.55050 / 0.28 (11920) hydrogen bonds : bond 0.03876 / 2.62 ( 556) hydrogen bonds : angle 3.99324 / 3.13 ( 1626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: A 86 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.7008 (t80) REVERT: A 123 GLN cc_start: 0.8035 (mp10) cc_final: 0.7783 (mp-120) REVERT: A 413 GLU cc_start: 0.7720 (mm-30) cc_final: 0.6880 (mm-30) REVERT: A 445 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: B 86 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.7442 (t80) REVERT: B 123 GLN cc_start: 0.7934 (mp10) cc_final: 0.7670 (mp-120) REVERT: B 151 MET cc_start: 0.8637 (mmm) cc_final: 0.8167 (mmm) REVERT: B 338 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7331 (mt) REVERT: B 385 ILE cc_start: 0.8575 (mm) cc_final: 0.8356 (mt) REVERT: B 439 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8193 (mtp) REVERT: B 546 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7820 (ptt-90) outliers start: 14 outliers final: 4 residues processed: 122 average time/residue: 0.4377 time to fit residues: 57.2118 Evaluate side-chains 121 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 546 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 ASN A 457 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.148174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108108 restraints weight = 7851.580| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.40 r_work: 0.3171 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8762 Z= 0.130 Angle : 0.553 7.130 11920 Z= 0.276 Chirality : 0.042 0.196 1390 Planarity : 0.006 0.059 1384 Dihedral : 10.236 89.701 1836 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.40 % Allowed : 10.70 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.27), residues: 1014 helix: 1.92 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.32 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 227 TYR 0.006 0.001 TYR B 332 PHE 0.019 0.001 PHE A 352 TRP 0.024 0.002 TRP A 418 HIS 0.019 0.003 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8762) covalent geometry : angle 0.55330 / 0.28 (11920) hydrogen bonds : bond 0.03840 / 2.60 ( 556) hydrogen bonds : angle 3.99308 / 3.13 ( 1626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.7020 (t80) REVERT: A 123 GLN cc_start: 0.8012 (mp10) cc_final: 0.7749 (mp-120) REVERT: A 227 ARG cc_start: 0.7229 (mtp-110) cc_final: 0.6756 (ttp-110) REVERT: A 338 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7215 (mt) REVERT: A 413 GLU cc_start: 0.7728 (mm-30) cc_final: 0.6894 (mm-30) REVERT: A 445 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: B 86 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.7450 (t80) REVERT: B 123 GLN cc_start: 0.7915 (mp10) cc_final: 0.7626 (mp-120) REVERT: B 151 MET cc_start: 0.8638 (mmm) cc_final: 0.8169 (mmm) REVERT: B 227 ARG cc_start: 0.6984 (mtp-110) cc_final: 0.6607 (ttp-110) REVERT: B 231 TRP cc_start: 0.8550 (OUTLIER) cc_final: 0.8057 (t-100) REVERT: B 338 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7348 (mt) REVERT: B 385 ILE cc_start: 0.8572 (mm) cc_final: 0.8357 (mt) REVERT: B 439 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8187 (mtp) REVERT: B 546 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7797 (ptt-90) outliers start: 12 outliers final: 2 residues processed: 122 average time/residue: 0.4644 time to fit residues: 60.9440 Evaluate side-chains 124 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 546 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 ASN A 457 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.148128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108091 restraints weight = 7861.360| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.39 r_work: 0.3174 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8762 Z= 0.131 Angle : 0.553 7.145 11920 Z= 0.276 Chirality : 0.042 0.196 1390 Planarity : 0.006 0.053 1384 Dihedral : 10.241 89.967 1836 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.51 % Allowed : 10.70 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.27), residues: 1014 helix: 1.90 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.31 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 227 TYR 0.006 0.001 TYR B 332 PHE 0.018 0.001 PHE A 352 TRP 0.024 0.002 TRP A 418 HIS 0.019 0.003 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8762) covalent geometry : angle 0.55337 / 0.28 (11920) hydrogen bonds : bond 0.03854 / 2.60 ( 556) hydrogen bonds : angle 3.99560 / 3.13 ( 1626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.6879 (t80) REVERT: A 123 GLN cc_start: 0.8006 (mp10) cc_final: 0.7738 (mp-120) REVERT: A 338 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7204 (mt) REVERT: A 413 GLU cc_start: 0.7696 (mm-30) cc_final: 0.6814 (mm-30) REVERT: A 445 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: B 86 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.7427 (t80) REVERT: B 123 GLN cc_start: 0.7903 (mp10) cc_final: 0.7641 (mp-120) REVERT: B 151 MET cc_start: 0.8623 (mmm) cc_final: 0.8152 (mmm) REVERT: B 227 ARG cc_start: 0.6979 (mtp-110) cc_final: 0.6601 (ttp-110) REVERT: B 231 TRP cc_start: 0.8532 (OUTLIER) cc_final: 0.8033 (t-100) REVERT: B 338 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7335 (mt) REVERT: B 385 ILE cc_start: 0.8558 (mm) cc_final: 0.8339 (mt) REVERT: B 439 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8182 (mtp) REVERT: B 546 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7866 (ptt-90) outliers start: 13 outliers final: 4 residues processed: 123 average time/residue: 0.4705 time to fit residues: 62.1595 Evaluate side-chains 126 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 546 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 ASN A 457 HIS B 457 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107193 restraints weight = 7860.804| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.40 r_work: 0.3162 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8762 Z= 0.142 Angle : 0.573 7.262 11920 Z= 0.285 Chirality : 0.043 0.190 1390 Planarity : 0.006 0.059 1384 Dihedral : 10.394 89.550 1836 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.51 % Allowed : 10.58 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.27), residues: 1014 helix: 1.85 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.33 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 227 TYR 0.007 0.001 TYR B 332 PHE 0.019 0.002 PHE A 352 TRP 0.026 0.002 TRP A 418 HIS 0.019 0.003 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 8762) covalent geometry : angle 0.57288 / 0.29 (11920) hydrogen bonds : bond 0.04024 / 2.71 ( 556) hydrogen bonds : angle 4.05558 / 3.16 ( 1626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.2700 (tpt) cc_final: 0.2379 (tpt) REVERT: A 55 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: A 86 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.6922 (t80) REVERT: A 123 GLN cc_start: 0.7983 (mp10) cc_final: 0.7719 (mp-120) REVERT: A 227 ARG cc_start: 0.7261 (mtp-110) cc_final: 0.6756 (ttp-110) REVERT: A 338 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7215 (mt) REVERT: A 413 GLU cc_start: 0.7710 (mm-30) cc_final: 0.6756 (tm-30) REVERT: A 445 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: B 86 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.7332 (t80) REVERT: B 123 GLN cc_start: 0.7907 (mp10) cc_final: 0.7634 (mp-120) REVERT: B 151 MET cc_start: 0.8630 (mmm) cc_final: 0.8169 (mmm) REVERT: B 227 ARG cc_start: 0.6976 (mtp-110) cc_final: 0.6615 (ttp-110) REVERT: B 231 TRP cc_start: 0.8534 (OUTLIER) cc_final: 0.7980 (t-100) REVERT: B 338 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7341 (mt) REVERT: B 385 ILE cc_start: 0.8561 (mm) cc_final: 0.8350 (mt) REVERT: B 439 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8164 (mtp) outliers start: 13 outliers final: 4 residues processed: 121 average time/residue: 0.4523 time to fit residues: 58.9326 Evaluate side-chains 124 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 231 TRP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 439 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.0060 chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 457 HIS B 457 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.147899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.107639 restraints weight = 7801.996| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.40 r_work: 0.3167 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8762 Z= 0.138 Angle : 0.565 7.150 11920 Z= 0.282 Chirality : 0.043 0.196 1390 Planarity : 0.006 0.059 1384 Dihedral : 10.456 89.705 1836 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.63 % Allowed : 10.47 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.27), residues: 1014 helix: 1.85 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.33 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 227 TYR 0.006 0.001 TYR B 332 PHE 0.018 0.002 PHE A 352 TRP 0.025 0.002 TRP A 418 HIS 0.018 0.004 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8762) covalent geometry : angle 0.56518 / 0.28 (11920) hydrogen bonds : bond 0.03939 / 2.65 ( 556) hydrogen bonds : angle 4.02876 / 3.14 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3727.06 seconds wall clock time: 64 minutes 3.76 seconds (3843.76 seconds total)