Starting phenix.real_space_refine on Wed Aug 5 18:36:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z62_73831/08_2026/9z62_73831_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z62_73831/08_2026/9z62_73831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z62_73831/08_2026/9z62_73831_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z62_73831/08_2026/9z62_73831_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z62_73831/08_2026/9z62_73831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z62_73831/08_2026/9z62_73831.map" } resolution = 3.1 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= 0.008 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: 7 Type Number sf(0) Gaussians P 1 5.49 5 S 28 5.16 5 Na 4 4.78 5 C 3495 2.51 5 N 863 2.21 5 O 968 1.98 5 H 5412 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10771 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 7217 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 19, 'TRANS': 444} Chain breaks: 2 Chain: "B" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1859 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1658 Classifications: {'peptide': 111} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 37 Unusual residues: {' NA': 4, 'CLR': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 1.86, per 1000 atoms: 0.17 Number of scatterers: 10771 At special positions: 0 Unit cell: (73.225, 79.025, 131.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 28 16.00 P 1 15.00 Na 4 11.00 O 968 8.00 N 863 7.00 C 3495 6.00 H 5412 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 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: 0.82 Conformation dependent library (CDL) restraints added in 213.2 milliseconds 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1282 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 58.5% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 67 through 104 removed outlier: 3.625A pdb=" N ALA A 73 " --> pdb=" O PHE A 69 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 147 Processing helix chain 'A' and resid 151 through 166 Proline residue: A 157 - end of helix removed outlier: 3.526A pdb=" N ILE A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 removed outlier: 3.706A pdb=" N THR A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 212 removed outlier: 4.511A pdb=" N HIS A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.722A pdb=" N MET A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 362 Processing helix chain 'A' and resid 364 through 376 removed outlier: 3.539A pdb=" N VAL A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 402 Processing helix chain 'A' and resid 403 through 417 removed outlier: 3.634A pdb=" N PHE A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 421 through 446 Proline residue: A 427 - end of helix removed outlier: 3.729A pdb=" N THR A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 474 removed outlier: 4.273A pdb=" N GLY A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASN A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 466 " --> pdb=" O HIS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.885A pdb=" N ARG A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 removed outlier: 4.222A pdb=" N ALA A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 removed outlier: 3.740A pdb=" N LEU A 513 " --> pdb=" O PHE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 550 Proline residue: A 532 - end of helix Processing helix chain 'A' and resid 556 through 560 removed outlier: 3.910A pdb=" N SER A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'B' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.288A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TRP B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.288A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR B 111 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.613A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 31 335 hydrogen bonds defined for protein. 951 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: 2.16 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5405 1.03 - 1.23: 13 1.23 - 1.42: 2232 1.42 - 1.62: 3197 1.62 - 1.81: 43 Bond restraints: 10890 Sorted by residual: bond pdb=" C LEU A 511 " pdb=" O LEU A 511 " ideal model delta sigma weight residual 1.244 1.218 0.026 9.80e-03 1.04e+04 6.77e+00 bond pdb=" N ASN B 35 " pdb=" CA ASN B 35 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.22e-02 6.72e+03 5.86e+00 bond pdb=" N ASN A 163 " pdb=" CA ASN A 163 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.21e+00 bond pdb=" C6 CLR A 706 " pdb=" C7 CLR A 706 " ideal model delta sigma weight residual 1.492 1.537 -0.045 2.00e-02 2.50e+03 4.95e+00 bond pdb=" CA SER B 71 " pdb=" CB SER B 71 " ideal model delta sigma weight residual 1.535 1.497 0.038 1.71e-02 3.42e+03 4.94e+00 ... (remaining 10885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 19361 1.53 - 3.07: 312 3.07 - 4.60: 30 4.60 - 6.14: 2 6.14 - 7.67: 2 Bond angle restraints: 19707 Sorted by residual: angle pdb=" CA LYS A 274 " pdb=" C LYS A 274 " pdb=" O LYS A 274 " ideal model delta sigma weight residual 121.19 117.40 3.79 1.10e+00 8.26e-01 1.19e+01 angle pdb=" CA SER B 71 " pdb=" C SER B 71 " pdb=" O SER B 71 " ideal model delta sigma weight residual 121.58 117.90 3.68 1.16e+00 7.43e-01 1.01e+01 angle pdb=" CA LYS B 87 " pdb=" C LYS B 87 " pdb=" O LYS B 87 " ideal model delta sigma weight residual 121.40 118.03 3.37 1.11e+00 8.12e-01 9.22e+00 angle pdb=" CA SER A 201 " pdb=" C SER A 201 " pdb=" O SER A 201 " ideal model delta sigma weight residual 120.55 117.42 3.13 1.06e+00 8.90e-01 8.74e+00 angle pdb=" CA ASN A 163 " pdb=" C ASN A 163 " pdb=" O ASN A 163 " ideal model delta sigma weight residual 120.55 117.68 2.87 1.06e+00 8.90e-01 7.35e+00 ... (remaining 19702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4606 17.64 - 35.29: 403 35.29 - 52.93: 140 52.93 - 70.58: 40 70.58 - 88.22: 4 Dihedral angle restraints: 5193 sinusoidal: 2816 harmonic: 2377 Sorted by residual: dihedral pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " pdb=" SG CYS A 321 " pdb=" CB CYS A 321 " ideal model delta sinusoidal sigma weight residual 93.00 134.66 -41.66 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CA CYS A 277 " pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " pdb=" SG CYS A 321 " ideal model delta sinusoidal sigma weight residual 79.00 12.65 66.35 1 2.00e+01 2.50e-03 1.44e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 64.82 28.18 1 1.00e+01 1.00e-02 1.14e+01 ... (remaining 5190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 824 0.073 - 0.146: 67 0.146 - 0.219: 0 0.219 - 0.292: 1 0.292 - 0.365: 3 Chirality restraints: 895 Sorted by residual: chirality pdb=" C17 CLR A 706 " pdb=" C13 CLR A 706 " pdb=" C16 CLR A 706 " pdb=" C20 CLR A 706 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C13 CLR A 706 " pdb=" C12 CLR A 706 " pdb=" C14 CLR A 706 " pdb=" C17 CLR A 706 " both_signs ideal model delta sigma weight residual False -2.93 -3.26 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C20 CLR A 706 " pdb=" C17 CLR A 706 " pdb=" C21 CLR A 706 " pdb=" C22 CLR A 706 " both_signs ideal model delta sigma weight residual False 2.59 2.91 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 892 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 35 " -0.184 2.00e-02 2.50e+03 2.03e-01 6.18e+02 pdb=" CG ASN B 35 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 35 " 0.176 2.00e-02 2.50e+03 pdb=" ND2 ASN B 35 " 0.005 2.00e-02 2.50e+03 pdb="HD21 ASN B 35 " -0.307 2.00e-02 2.50e+03 pdb="HD22 ASN B 35 " 0.297 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 163 " 0.156 2.00e-02 2.50e+03 1.65e-01 4.06e+02 pdb=" CG ASN A 163 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 163 " -0.140 2.00e-02 2.50e+03 pdb=" ND2 ASN A 163 " -0.006 2.00e-02 2.50e+03 pdb="HD21 ASN A 163 " 0.249 2.00e-02 2.50e+03 pdb="HD22 ASN A 163 " -0.237 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 71 " 0.014 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" N LEU B 72 " -0.045 2.00e-02 2.50e+03 pdb=" CA LEU B 72 " 0.012 2.00e-02 2.50e+03 pdb=" H LEU B 72 " 0.020 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 213 2.12 - 2.74: 19570 2.74 - 3.36: 32327 3.36 - 3.98: 40047 3.98 - 4.60: 62814 Nonbonded interactions: 154971 Sorted by model distance: nonbonded pdb=" OE1 GLN A 552 " pdb=" H GLN A 552 " model vdw 1.503 2.450 nonbonded pdb="HE21 GLN A 547 " pdb=" O LEU A 558 " model vdw 1.646 2.450 nonbonded pdb=" OG1 THR C 89 " pdb=" HZ3 LYS C 107 " model vdw 1.647 2.450 nonbonded pdb=" O PHE B 29 " pdb=" HG1 THR B 53 " model vdw 1.650 2.450 nonbonded pdb=" O LEU A 566 " pdb=" HG SER A 570 " model vdw 1.731 2.450 ... (remaining 154966 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: 0.010 Normalize map: mean=0, sd=1: 3.810 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: 0.060 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 0.003 0.045 5481 Z= 0.171 Angle : 0.512 7.670 7475 Z= 0.280 Chirality : 0.043 0.365 895 Planarity : 0.004 0.048 913 Dihedral : 15.067 88.224 1965 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.68 % Allowed : 18.97 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.79 (0.34), residues: 686 helix: 2.85 (0.28), residues: 353 sheet: 1.46 (0.50), residues: 122 loop : 0.35 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 576 TYR 0.007 0.001 TYR A 474 PHE 0.005 0.001 PHE B 68 TRP 0.013 0.001 TRP B 50 HIS 0.003 0.000 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.17 ( 5478) covalent geometry : angle 0.51183 / 0.28 ( 7469) SS BOND : bond 0.00147 / 0.07 ( 3) SS BOND : angle 0.44806 / 0.24 ( 6) hydrogen bonds : bond 0.15361 / 9.58 ( 331) hydrogen bonds : angle 6.12969 / 4.51 ( 951) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.3841 (OUTLIER) cc_final: 0.3581 (tm) REVERT: B 3 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7587 (mt0) REVERT: B 13 LYS cc_start: 0.7040 (mttm) cc_final: 0.6754 (mtpt) REVERT: B 87 LYS cc_start: 0.7209 (ptpp) cc_final: 0.6920 (mttm) REVERT: C 46 GLN cc_start: 0.7194 (mt0) cc_final: 0.6949 (mm110) REVERT: C 106 THR cc_start: 0.8124 (m) cc_final: 0.7763 (p) outliers start: 4 outliers final: 3 residues processed: 105 average time/residue: 0.1445 time to fit residues: 20.4284 Evaluate side-chains 91 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 50 TRP Chi-restraints excluded: chain B residue 71 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 ASN B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.200758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.167575 restraints weight = 15853.105| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.90 r_work: 0.3751 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5481 Z= 0.175 Angle : 0.530 4.841 7475 Z= 0.285 Chirality : 0.040 0.163 895 Planarity : 0.004 0.037 913 Dihedral : 4.967 47.134 804 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.56 % Allowed : 18.12 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.44 (0.34), residues: 686 helix: 2.45 (0.28), residues: 358 sheet: 1.95 (0.52), residues: 111 loop : 0.01 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 67 TYR 0.020 0.002 TYR C 53 PHE 0.011 0.001 PHE B 95 TRP 0.014 0.001 TRP B 112 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 5478) covalent geometry : angle 0.53020 / 0.28 ( 7469) SS BOND : bond 0.00286 / 0.14 ( 3) SS BOND : angle 0.79394 / 0.47 ( 6) hydrogen bonds : bond 0.04368 / 2.80 ( 331) hydrogen bonds : angle 4.90858 / 3.52 ( 951) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.3987 (OUTLIER) cc_final: 0.3753 (tm) REVERT: A 274 LYS cc_start: 0.5827 (OUTLIER) cc_final: 0.5576 (tttt) REVERT: A 581 ILE cc_start: 0.8307 (tp) cc_final: 0.7855 (pt) REVERT: B 3 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7848 (mt0) REVERT: B 82 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: B 90 ASP cc_start: 0.7445 (m-30) cc_final: 0.7095 (t0) outliers start: 15 outliers final: 6 residues processed: 98 average time/residue: 0.1423 time to fit residues: 18.6836 Evaluate side-chains 92 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain C residue 41 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.196849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.162516 restraints weight = 16031.108| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.95 r_work: 0.3694 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5481 Z= 0.170 Angle : 0.495 5.870 7475 Z= 0.263 Chirality : 0.039 0.155 895 Planarity : 0.004 0.036 913 Dihedral : 4.805 49.775 800 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.05 % Allowed : 17.61 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.33), residues: 686 helix: 2.37 (0.28), residues: 358 sheet: 1.91 (0.51), residues: 111 loop : -0.04 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 65 TYR 0.011 0.001 TYR C 90 PHE 0.009 0.001 PHE B 95 TRP 0.008 0.001 TRP B 36 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 5478) covalent geometry : angle 0.49443 / 0.26 ( 7469) SS BOND : bond 0.00241 / 0.12 ( 3) SS BOND : angle 0.60475 / 0.34 ( 6) hydrogen bonds : bond 0.04456 / 2.86 ( 331) hydrogen bonds : angle 4.77963 / 3.44 ( 951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7048 (tpp) cc_final: 0.6818 (tpt) REVERT: A 159 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7208 (mm) REVERT: A 238 LEU cc_start: 0.3984 (OUTLIER) cc_final: 0.3771 (tm) REVERT: A 274 LYS cc_start: 0.5915 (OUTLIER) cc_final: 0.5530 (tttt) REVERT: A 434 ILE cc_start: 0.8131 (mm) cc_final: 0.7917 (mm) REVERT: A 544 ASN cc_start: 0.8410 (m110) cc_final: 0.8146 (m-40) REVERT: A 581 ILE cc_start: 0.8317 (tp) cc_final: 0.7812 (pt) REVERT: B 3 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7851 (mt0) outliers start: 12 outliers final: 6 residues processed: 97 average time/residue: 0.1324 time to fit residues: 17.5702 Evaluate side-chains 92 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain C residue 41 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 57 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.0010 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.194054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.162637 restraints weight = 16002.276| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.75 r_work: 0.3634 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5481 Z= 0.138 Angle : 0.472 4.893 7475 Z= 0.252 Chirality : 0.039 0.147 895 Planarity : 0.004 0.050 913 Dihedral : 4.823 58.474 800 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.71 % Allowed : 17.61 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.26 (0.33), residues: 686 helix: 2.38 (0.28), residues: 356 sheet: 1.87 (0.51), residues: 110 loop : -0.20 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 67 TYR 0.012 0.001 TYR C 53 PHE 0.009 0.001 PHE B 68 TRP 0.015 0.001 TRP A 567 HIS 0.005 0.002 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 5478) covalent geometry : angle 0.47224 / 0.25 ( 7469) SS BOND : bond 0.00161 / 0.08 ( 3) SS BOND : angle 0.52616 / 0.30 ( 6) hydrogen bonds : bond 0.03963 / 2.57 ( 331) hydrogen bonds : angle 4.62392 / 3.34 ( 951) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.7076 (tpp) cc_final: 0.6795 (tpt) REVERT: A 159 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7232 (mm) REVERT: A 226 PHE cc_start: 0.6484 (m-10) cc_final: 0.6108 (m-10) REVERT: A 274 LYS cc_start: 0.5989 (OUTLIER) cc_final: 0.5523 (tttp) REVERT: A 544 ASN cc_start: 0.8493 (m110) cc_final: 0.8122 (m-40) REVERT: B 3 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7810 (mt0) outliers start: 10 outliers final: 6 residues processed: 94 average time/residue: 0.1238 time to fit residues: 15.5542 Evaluate side-chains 90 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 41 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.0060 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.195411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.160971 restraints weight = 15938.839| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.93 r_work: 0.3681 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5481 Z= 0.124 Angle : 0.463 4.854 7475 Z= 0.244 Chirality : 0.038 0.147 895 Planarity : 0.004 0.037 913 Dihedral : 4.618 57.962 797 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.71 % Allowed : 18.97 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.22 (0.33), residues: 686 helix: 2.35 (0.28), residues: 357 sheet: 1.83 (0.51), residues: 109 loop : -0.20 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.011 0.001 TYR C 53 PHE 0.008 0.001 PHE B 68 TRP 0.014 0.001 TRP A 567 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 5478) covalent geometry : angle 0.46335 / 0.24 ( 7469) SS BOND : bond 0.00153 / 0.08 ( 3) SS BOND : angle 0.45990 / 0.25 ( 6) hydrogen bonds : bond 0.03877 / 2.53 ( 331) hydrogen bonds : angle 4.54107 / 3.28 ( 951) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7016 (tpp) cc_final: 0.6766 (tpt) REVERT: A 226 PHE cc_start: 0.6463 (m-10) cc_final: 0.6121 (m-10) REVERT: A 274 LYS cc_start: 0.6036 (OUTLIER) cc_final: 0.5580 (tttp) REVERT: A 544 ASN cc_start: 0.8505 (m110) cc_final: 0.8155 (m-40) REVERT: B 59 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7913 (m) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.1405 time to fit residues: 17.5553 Evaluate side-chains 92 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 41 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.190772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156889 restraints weight = 16479.211| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.07 r_work: 0.3171 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5481 Z= 0.175 Angle : 0.500 5.363 7475 Z= 0.268 Chirality : 0.039 0.149 895 Planarity : 0.004 0.036 913 Dihedral : 4.595 45.802 797 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.88 % Allowed : 19.66 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.33), residues: 686 helix: 2.13 (0.27), residues: 359 sheet: 1.56 (0.51), residues: 109 loop : -0.26 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 54 TYR 0.018 0.002 TYR B 101 PHE 0.012 0.001 PHE A 378 TRP 0.016 0.002 TRP A 567 HIS 0.005 0.002 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 5478) covalent geometry : angle 0.49987 / 0.27 ( 7469) SS BOND : bond 0.00241 / 0.12 ( 3) SS BOND : angle 0.54879 / 0.30 ( 6) hydrogen bonds : bond 0.04253 / 2.75 ( 331) hydrogen bonds : angle 4.70355 / 3.41 ( 951) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.6981 (tpp) cc_final: 0.6685 (tpt) REVERT: A 226 PHE cc_start: 0.6357 (m-10) cc_final: 0.6090 (m-10) REVERT: A 274 LYS cc_start: 0.5959 (OUTLIER) cc_final: 0.5395 (tttp) REVERT: A 365 GLN cc_start: 0.6576 (tt0) cc_final: 0.6208 (mp10) REVERT: C 17 GLN cc_start: 0.5876 (tt0) cc_final: 0.5252 (tp-100) outliers start: 11 outliers final: 7 residues processed: 95 average time/residue: 0.1489 time to fit residues: 18.5554 Evaluate side-chains 90 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 41 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.0030 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN C 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.190853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.156432 restraints weight = 16368.823| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.13 r_work: 0.3616 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5481 Z= 0.137 Angle : 0.472 5.146 7475 Z= 0.250 Chirality : 0.038 0.144 895 Planarity : 0.004 0.037 913 Dihedral : 4.514 45.726 797 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.22 % Allowed : 18.97 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.00 (0.33), residues: 686 helix: 2.21 (0.27), residues: 360 sheet: 1.53 (0.52), residues: 109 loop : -0.30 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 67 TYR 0.015 0.001 TYR B 101 PHE 0.009 0.001 PHE B 68 TRP 0.018 0.001 TRP A 567 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 5478) covalent geometry : angle 0.47239 / 0.25 ( 7469) SS BOND : bond 0.00179 / 0.09 ( 3) SS BOND : angle 0.46603 / 0.25 ( 6) hydrogen bonds : bond 0.03967 / 2.59 ( 331) hydrogen bonds : angle 4.60393 / 3.34 ( 951) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7112 (tpp) cc_final: 0.6823 (tpt) REVERT: A 226 PHE cc_start: 0.6434 (m-10) cc_final: 0.6140 (m-10) REVERT: A 274 LYS cc_start: 0.6172 (OUTLIER) cc_final: 0.5610 (tttp) REVERT: B 59 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.8058 (m) REVERT: C 17 GLN cc_start: 0.6050 (tt0) cc_final: 0.5448 (tp-100) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.1410 time to fit residues: 16.4173 Evaluate side-chains 85 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.0670 chunk 53 optimal weight: 0.3980 chunk 46 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.191357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.157266 restraints weight = 16330.825| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.10 r_work: 0.3634 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5481 Z= 0.115 Angle : 0.455 5.003 7475 Z= 0.240 Chirality : 0.038 0.141 895 Planarity : 0.004 0.037 913 Dihedral : 4.453 47.162 797 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.88 % Allowed : 19.15 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.14 (0.34), residues: 686 helix: 2.35 (0.28), residues: 360 sheet: 1.59 (0.52), residues: 109 loop : -0.29 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 54 TYR 0.015 0.001 TYR B 101 PHE 0.014 0.001 PHE A 96 TRP 0.014 0.001 TRP A 567 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 5478) covalent geometry : angle 0.45506 / 0.24 ( 7469) SS BOND : bond 0.00143 / 0.07 ( 3) SS BOND : angle 0.43680 / 0.23 ( 6) hydrogen bonds : bond 0.03762 / 2.47 ( 331) hydrogen bonds : angle 4.47500 / 3.25 ( 951) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7082 (tpp) cc_final: 0.6805 (tpt) REVERT: A 226 PHE cc_start: 0.6407 (m-10) cc_final: 0.6116 (m-10) REVERT: A 274 LYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5633 (tttp) REVERT: B 73 GLU cc_start: 0.7066 (tt0) cc_final: 0.6788 (tt0) REVERT: C 17 GLN cc_start: 0.6081 (tt0) cc_final: 0.5470 (tp-100) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.1400 time to fit residues: 15.4051 Evaluate side-chains 83 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.190818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.156604 restraints weight = 16280.004| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.12 r_work: 0.3667 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5481 Z= 0.117 Angle : 0.454 4.976 7475 Z= 0.238 Chirality : 0.038 0.140 895 Planarity : 0.004 0.037 913 Dihedral : 4.410 46.291 797 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.54 % Allowed : 19.32 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.16 (0.34), residues: 686 helix: 2.38 (0.28), residues: 360 sheet: 1.58 (0.52), residues: 109 loop : -0.30 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 54 TYR 0.013 0.001 TYR B 101 PHE 0.012 0.001 PHE A 96 TRP 0.012 0.001 TRP A 567 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 5478) covalent geometry : angle 0.45427 / 0.24 ( 7469) SS BOND : bond 0.00156 / 0.08 ( 3) SS BOND : angle 0.44505 / 0.24 ( 6) hydrogen bonds : bond 0.03752 / 2.46 ( 331) hydrogen bonds : angle 4.43854 / 3.22 ( 951) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.7125 (tpp) cc_final: 0.6864 (tpt) REVERT: A 226 PHE cc_start: 0.6505 (m-10) cc_final: 0.6237 (m-10) REVERT: A 274 LYS cc_start: 0.6346 (OUTLIER) cc_final: 0.5773 (tttp) REVERT: B 73 GLU cc_start: 0.7177 (tt0) cc_final: 0.6921 (tt0) REVERT: C 17 GLN cc_start: 0.6119 (tt0) cc_final: 0.5501 (tp-100) outliers start: 9 outliers final: 8 residues processed: 86 average time/residue: 0.1142 time to fit residues: 13.4186 Evaluate side-chains 85 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 45 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 20 optimal weight: 0.0370 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 overall best weight: 0.2458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.192595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157962 restraints weight = 16372.258| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.02 r_work: 0.3317 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5481 Z= 0.095 Angle : 0.446 4.869 7475 Z= 0.233 Chirality : 0.037 0.138 895 Planarity : 0.004 0.037 913 Dihedral : 4.337 47.465 797 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.37 % Allowed : 19.66 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.29 (0.34), residues: 686 helix: 2.51 (0.28), residues: 360 sheet: 1.65 (0.51), residues: 109 loop : -0.28 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 18 TYR 0.018 0.001 TYR B 101 PHE 0.011 0.001 PHE A 96 TRP 0.013 0.001 TRP A 567 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 ( 5478) covalent geometry : angle 0.44642 / 0.23 ( 7469) SS BOND : bond 0.00117 / 0.06 ( 3) SS BOND : angle 0.42833 / 0.23 ( 6) hydrogen bonds : bond 0.03533 / 2.33 ( 331) hydrogen bonds : angle 4.32996 / 3.14 ( 951) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.6927 (tpp) cc_final: 0.6652 (tpt) REVERT: A 226 PHE cc_start: 0.6318 (m-10) cc_final: 0.6048 (m-10) REVERT: A 274 LYS cc_start: 0.5890 (OUTLIER) cc_final: 0.5297 (tttp) REVERT: B 73 GLU cc_start: 0.6853 (tt0) cc_final: 0.6544 (tt0) REVERT: C 17 GLN cc_start: 0.5873 (tt0) cc_final: 0.5195 (tp-100) outliers start: 8 outliers final: 7 residues processed: 81 average time/residue: 0.1123 time to fit residues: 12.4889 Evaluate side-chains 83 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 16 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.190508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.156702 restraints weight = 16483.213| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.12 r_work: 0.3307 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5481 Z= 0.126 Angle : 0.463 5.012 7475 Z= 0.244 Chirality : 0.038 0.145 895 Planarity : 0.004 0.037 913 Dihedral : 4.379 46.474 797 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.71 % Allowed : 18.97 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.22 (0.34), residues: 686 helix: 2.51 (0.28), residues: 358 sheet: 1.57 (0.52), residues: 109 loop : -0.39 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 54 TYR 0.018 0.001 TYR B 101 PHE 0.012 0.001 PHE A 96 TRP 0.011 0.001 TRP A 567 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 5478) covalent geometry : angle 0.46266 / 0.24 ( 7469) SS BOND : bond 0.00167 / 0.08 ( 3) SS BOND : angle 0.46164 / 0.25 ( 6) hydrogen bonds : bond 0.03736 / 2.43 ( 331) hydrogen bonds : angle 4.38908 / 3.18 ( 951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2963.43 seconds wall clock time: 50 minutes 45.25 seconds (3045.25 seconds total)