Starting phenix.real_space_refine on Wed Sep 17 05:33:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dng_47040/09_2025/9dng_47040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dng_47040/09_2025/9dng_47040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dng_47040/09_2025/9dng_47040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dng_47040/09_2025/9dng_47040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dng_47040/09_2025/9dng_47040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dng_47040/09_2025/9dng_47040.map" } resolution = 3.52 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= 0.009 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 3344 2.51 5 N 885 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5252 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 3463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3463 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 415} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 1.41, per 1000 atoms: 0.27 Number of scatterers: 5252 At special positions: 0 Unit cell: (62.208, 111.974, 116.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 1005 8.00 N 885 7.00 C 3344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 225.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1272 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 12 sheets defined 20.7% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'H' and resid 31 through 35 Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.533A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing helix chain 'H' and resid 107 through 112 removed outlier: 4.146A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 98 removed outlier: 4.357A pdb=" N VAL L 98 " --> pdb=" O TYR L 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.514A pdb=" N ASN A 162 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 163 " --> pdb=" O LYS A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 163' Processing helix chain 'A' and resid 179 through 196 Processing helix chain 'A' and resid 198 through 218 removed outlier: 3.647A pdb=" N VAL A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 258 Processing helix chain 'A' and resid 259 through 282 removed outlier: 3.619A pdb=" N LEU A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 413 through 416 Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.529A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 Processing sheet with id=AA3, first strand: chain 'H' and resid 61 through 63 removed outlier: 3.940A pdb=" N SER H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA H 100 " --> pdb=" O HIS H 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.643A pdb=" N THR L 6 " --> pdb=" O ARG L 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.887A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.677A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 113 through 117 removed outlier: 3.698A pdb=" N GLY A 39 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 40 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 9 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 26 through 28 Processing sheet with id=AA9, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.531A pdb=" N ARG A 52 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 58 through 62 removed outlier: 3.721A pdb=" N ARG A 62 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 141 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 127 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 284 through 289 removed outlier: 3.501A pdb=" N THR A 287 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN A 323 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 367 " --> pdb=" O ASN A 323 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 308 through 310 removed outlier: 5.672A pdb=" N TYR A 309 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR A 422 " --> pdb=" O PHE A 450 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU A 452 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N VAL A 420 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 423 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 332 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 358 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE A 334 " --> pdb=" O MET A 356 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N MET A 356 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 336 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 340 " --> pdb=" O TYR A 350 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1689 1.34 - 1.46: 1143 1.46 - 1.58: 2507 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 5364 Sorted by residual: bond pdb=" N ASP A 35 " pdb=" CA ASP A 35 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.29e-02 6.01e+03 5.39e+00 bond pdb=" N PHE A 87 " pdb=" CA PHE A 87 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.41e-02 5.03e+03 4.61e+00 bond pdb=" C ASP A 35 " pdb=" N PRO A 36 " ideal model delta sigma weight residual 1.329 1.348 -0.020 1.20e-02 6.94e+03 2.66e+00 bond pdb=" C CYS A 352 " pdb=" O CYS A 352 " ideal model delta sigma weight residual 1.249 1.236 0.012 8.50e-03 1.38e+04 2.15e+00 bond pdb=" C PRO A 88 " pdb=" N PRO A 89 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.25e-02 6.40e+03 1.87e+00 ... (remaining 5359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 7131 1.93 - 3.85: 126 3.85 - 5.78: 16 5.78 - 7.71: 3 7.71 - 9.63: 2 Bond angle restraints: 7278 Sorted by residual: angle pdb=" CB MET A 234 " pdb=" CG MET A 234 " pdb=" SD MET A 234 " ideal model delta sigma weight residual 112.70 122.33 -9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CA ASN A 162 " pdb=" C ASN A 162 " pdb=" O ASN A 162 " ideal model delta sigma weight residual 119.51 122.19 -2.68 1.04e+00 9.25e-01 6.62e+00 angle pdb=" CA LEU A 179 " pdb=" CB LEU A 179 " pdb=" CG LEU A 179 " ideal model delta sigma weight residual 116.30 124.91 -8.61 3.50e+00 8.16e-02 6.05e+00 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 125.87 -4.33 1.91e+00 2.74e-01 5.14e+00 angle pdb=" N VAL H 33 " pdb=" CA VAL H 33 " pdb=" C VAL H 33 " ideal model delta sigma weight residual 113.00 110.22 2.78 1.30e+00 5.92e-01 4.58e+00 ... (remaining 7273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 2833 17.36 - 34.72: 294 34.72 - 52.08: 86 52.08 - 69.44: 19 69.44 - 86.80: 9 Dihedral angle restraints: 3241 sinusoidal: 1271 harmonic: 1970 Sorted by residual: dihedral pdb=" CA LEU A 79 " pdb=" C LEU A 79 " pdb=" N PHE A 80 " pdb=" CA PHE A 80 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA GLN L 80 " pdb=" C GLN L 80 " pdb=" N PRO L 81 " pdb=" CA PRO L 81 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA SER L 77 " pdb=" C SER L 77 " pdb=" N SER L 78 " pdb=" CA SER L 78 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 3238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 523 0.031 - 0.063: 174 0.063 - 0.094: 71 0.094 - 0.125: 45 0.125 - 0.156: 9 Chirality restraints: 822 Sorted by residual: chirality pdb=" CG LEU L 12 " pdb=" CB LEU L 12 " pdb=" CD1 LEU L 12 " pdb=" CD2 LEU L 12 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA ILE L 22 " pdb=" N ILE L 22 " pdb=" C ILE L 22 " pdb=" CB ILE L 22 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA PRO L 81 " pdb=" N PRO L 81 " pdb=" C PRO L 81 " pdb=" CB PRO L 81 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 819 not shown) Planarity restraints: 932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO H 109 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 313 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO A 314 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 314 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 314 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 162 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C ASN A 162 " -0.023 2.00e-02 2.50e+03 pdb=" O ASN A 162 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A 163 " 0.008 2.00e-02 2.50e+03 ... (remaining 929 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 716 2.76 - 3.29: 4851 3.29 - 3.83: 8086 3.83 - 4.36: 9340 4.36 - 4.90: 16500 Nonbonded interactions: 39493 Sorted by model distance: nonbonded pdb=" OH TYR A 54 " pdb=" OD1 ASN A 83 " model vdw 2.221 3.040 nonbonded pdb=" NE2 GLN L 91 " pdb=" O LEU L 97 " model vdw 2.228 3.120 nonbonded pdb=" O LYS A 271 " pdb=" ND2 ASN A 275 " model vdw 2.250 3.120 nonbonded pdb=" O THR A 328 " pdb=" OG SER A 431 " model vdw 2.274 3.040 nonbonded pdb=" NH1 ARG A 210 " pdb=" OD2 ASP A 249 " model vdw 2.297 3.120 ... (remaining 39488 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 group one per residue 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.040 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 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 0.033 5366 Z= 0.160 Angle : 0.632 9.635 7282 Z= 0.329 Chirality : 0.044 0.156 822 Planarity : 0.004 0.040 932 Dihedral : 16.576 86.798 1963 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.35 % Allowed : 22.07 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.93 (0.33), residues: 661 helix: 2.87 (0.55), residues: 93 sheet: -0.79 (0.32), residues: 269 loop : -1.56 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 289 TYR 0.015 0.002 TYR A 54 PHE 0.016 0.002 PHE A 369 TRP 0.006 0.001 TRP H 111 HIS 0.002 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 5364) covalent geometry : angle 0.63251 ( 7278) SS BOND : bond 0.00361 ( 2) SS BOND : angle 0.27921 ( 4) hydrogen bonds : bond 0.23897 ( 201) hydrogen bonds : angle 8.96349 ( 555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.206 Fit side-chains REVERT: L 5 MET cc_start: 0.7341 (mmp) cc_final: 0.7103 (mmm) REVERT: L 53 SER cc_start: 0.7691 (p) cc_final: 0.7253 (t) REVERT: A 105 ILE cc_start: 0.5763 (OUTLIER) cc_final: 0.5354 (mt) REVERT: A 184 GLU cc_start: 0.6944 (tp30) cc_final: 0.6065 (tp30) REVERT: A 327 LYS cc_start: 0.6928 (mttt) cc_final: 0.6648 (mtpp) REVERT: A 357 GLU cc_start: 0.7369 (tp30) cc_final: 0.7152 (tp30) REVERT: A 360 ASP cc_start: 0.6301 (p0) cc_final: 0.5809 (p0) outliers start: 2 outliers final: 0 residues processed: 128 average time/residue: 0.0928 time to fit residues: 14.8430 Evaluate side-chains 123 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.0770 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 247 GLN A 264 GLN A 338 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.157427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134041 restraints weight = 7827.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137586 restraints weight = 4591.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140210 restraints weight = 3159.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141682 restraints weight = 2402.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.143084 restraints weight = 1987.830| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5366 Z= 0.127 Angle : 0.596 6.962 7282 Z= 0.314 Chirality : 0.045 0.150 822 Planarity : 0.004 0.041 932 Dihedral : 5.054 28.930 728 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.93 % Allowed : 20.67 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.52 (0.34), residues: 661 helix: 2.92 (0.56), residues: 95 sheet: -0.23 (0.32), residues: 279 loop : -1.59 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 289 TYR 0.025 0.002 TYR A 54 PHE 0.026 0.002 PHE A 369 TRP 0.009 0.001 TRP L 36 HIS 0.002 0.000 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5364) covalent geometry : angle 0.59583 ( 7278) SS BOND : bond 0.00319 ( 2) SS BOND : angle 0.33836 ( 4) hydrogen bonds : bond 0.04969 ( 201) hydrogen bonds : angle 6.16696 ( 555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 113 TYR cc_start: 0.6786 (m-80) cc_final: 0.6554 (m-10) REVERT: A 184 GLU cc_start: 0.6850 (tp30) cc_final: 0.5921 (tp30) REVERT: A 275 ASN cc_start: 0.8489 (m-40) cc_final: 0.7867 (m110) REVERT: A 316 SER cc_start: 0.7448 (OUTLIER) cc_final: 0.7114 (p) REVERT: A 327 LYS cc_start: 0.6824 (mttt) cc_final: 0.6574 (mtpp) REVERT: A 338 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7786 (tp40) outliers start: 11 outliers final: 4 residues processed: 126 average time/residue: 0.0923 time to fit residues: 14.5530 Evaluate side-chains 115 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 374 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 14 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.155790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.134007 restraints weight = 7724.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137798 restraints weight = 4290.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140442 restraints weight = 2833.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.141986 restraints weight = 2074.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143011 restraints weight = 1683.029| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5366 Z= 0.181 Angle : 0.623 7.490 7282 Z= 0.326 Chirality : 0.045 0.152 822 Planarity : 0.004 0.045 932 Dihedral : 5.123 23.475 726 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.33 % Allowed : 21.54 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.58 (0.34), residues: 661 helix: 2.89 (0.55), residues: 95 sheet: -0.26 (0.33), residues: 262 loop : -1.58 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.022 0.002 TYR A 54 PHE 0.024 0.002 PHE A 369 TRP 0.008 0.002 TRP H 117 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 5364) covalent geometry : angle 0.62278 ( 7278) SS BOND : bond 0.00485 ( 2) SS BOND : angle 0.20783 ( 4) hydrogen bonds : bond 0.05274 ( 201) hydrogen bonds : angle 5.83994 ( 555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.6325 (t70) cc_final: 0.5921 (t0) REVERT: A 105 ILE cc_start: 0.5898 (OUTLIER) cc_final: 0.5428 (mt) REVERT: A 113 TYR cc_start: 0.6924 (m-80) cc_final: 0.6650 (m-10) REVERT: A 275 ASN cc_start: 0.8518 (m-40) cc_final: 0.8003 (m110) REVERT: A 287 THR cc_start: 0.8110 (p) cc_final: 0.7786 (p) REVERT: A 316 SER cc_start: 0.7405 (OUTLIER) cc_final: 0.7160 (p) REVERT: A 327 LYS cc_start: 0.6396 (mttt) cc_final: 0.6046 (mtpp) REVERT: A 338 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7675 (tp40) outliers start: 19 outliers final: 9 residues processed: 139 average time/residue: 0.0848 time to fit residues: 14.8323 Evaluate side-chains 135 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 0.0570 chunk 61 optimal weight: 0.0170 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN A 247 GLN A 264 GLN A 320 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134890 restraints weight = 7706.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.138622 restraints weight = 4257.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141313 restraints weight = 2810.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.142872 restraints weight = 2060.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.144105 restraints weight = 1662.944| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5366 Z= 0.186 Angle : 0.625 7.830 7282 Z= 0.327 Chirality : 0.045 0.153 822 Planarity : 0.004 0.046 932 Dihedral : 5.167 23.264 726 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.08 % Allowed : 19.61 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.70 (0.33), residues: 661 helix: 2.72 (0.54), residues: 95 sheet: -0.33 (0.33), residues: 262 loop : -1.63 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 101 TYR 0.020 0.002 TYR A 54 PHE 0.023 0.002 PHE A 369 TRP 0.009 0.002 TRP H 117 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 5364) covalent geometry : angle 0.62478 ( 7278) SS BOND : bond 0.00397 ( 2) SS BOND : angle 0.23235 ( 4) hydrogen bonds : bond 0.05165 ( 201) hydrogen bonds : angle 5.71758 ( 555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 53 SER cc_start: 0.7527 (p) cc_final: 0.7113 (t) REVERT: L 104 THR cc_start: 0.7982 (p) cc_final: 0.7551 (t) REVERT: A 35 ASP cc_start: 0.8161 (t0) cc_final: 0.7924 (t0) REVERT: A 105 ILE cc_start: 0.5867 (OUTLIER) cc_final: 0.5427 (mt) REVERT: A 113 TYR cc_start: 0.6967 (m-10) cc_final: 0.6680 (m-10) REVERT: A 275 ASN cc_start: 0.8548 (m-40) cc_final: 0.8026 (m110) REVERT: A 286 GLU cc_start: 0.6752 (mp0) cc_final: 0.6540 (mp0) REVERT: A 316 SER cc_start: 0.7422 (OUTLIER) cc_final: 0.7187 (p) REVERT: A 327 LYS cc_start: 0.6436 (mttt) cc_final: 0.6068 (mtpt) REVERT: A 357 GLU cc_start: 0.7644 (tp30) cc_final: 0.7256 (tp30) outliers start: 29 outliers final: 18 residues processed: 152 average time/residue: 0.0866 time to fit residues: 16.5745 Evaluate side-chains 146 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 33 optimal weight: 0.0010 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133909 restraints weight = 7753.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137585 restraints weight = 4234.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140302 restraints weight = 2789.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141859 restraints weight = 2034.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.143240 restraints weight = 1641.052| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5366 Z= 0.223 Angle : 0.645 8.212 7282 Z= 0.340 Chirality : 0.046 0.153 822 Planarity : 0.004 0.048 932 Dihedral : 5.403 24.229 726 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.73 % Allowed : 21.02 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.79 (0.33), residues: 661 helix: 2.65 (0.53), residues: 95 sheet: -0.43 (0.33), residues: 268 loop : -1.67 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 41 TYR 0.021 0.002 TYR A 422 PHE 0.019 0.003 PHE A 369 TRP 0.010 0.002 TRP H 117 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 5364) covalent geometry : angle 0.64550 ( 7278) SS BOND : bond 0.00415 ( 2) SS BOND : angle 0.28259 ( 4) hydrogen bonds : bond 0.05488 ( 201) hydrogen bonds : angle 5.82703 ( 555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: L 53 SER cc_start: 0.7652 (p) cc_final: 0.7236 (t) REVERT: A 35 ASP cc_start: 0.8222 (t0) cc_final: 0.7928 (t0) REVERT: A 105 ILE cc_start: 0.5955 (OUTLIER) cc_final: 0.5497 (mt) REVERT: A 113 TYR cc_start: 0.6928 (m-10) cc_final: 0.6656 (m-10) REVERT: A 249 ASP cc_start: 0.7420 (t70) cc_final: 0.7186 (t0) REVERT: A 275 ASN cc_start: 0.8555 (m-40) cc_final: 0.8067 (m110) REVERT: A 316 SER cc_start: 0.7445 (OUTLIER) cc_final: 0.7123 (p) REVERT: A 327 LYS cc_start: 0.6476 (mttt) cc_final: 0.6155 (mtpp) REVERT: A 338 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7539 (tp40) outliers start: 27 outliers final: 20 residues processed: 151 average time/residue: 0.0900 time to fit residues: 17.0714 Evaluate side-chains 151 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 48 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 43 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.156785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135311 restraints weight = 7752.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.139242 restraints weight = 4228.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.141914 restraints weight = 2743.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143539 restraints weight = 1998.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144899 restraints weight = 1610.464| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5366 Z= 0.167 Angle : 0.614 8.111 7282 Z= 0.321 Chirality : 0.045 0.150 822 Planarity : 0.004 0.046 932 Dihedral : 5.176 22.722 726 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.55 % Allowed : 22.42 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.71 (0.33), residues: 661 helix: 2.63 (0.53), residues: 95 sheet: -0.29 (0.33), residues: 262 loop : -1.68 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 337 TYR 0.016 0.002 TYR A 422 PHE 0.019 0.002 PHE A 369 TRP 0.008 0.002 TRP H 111 HIS 0.002 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 5364) covalent geometry : angle 0.61441 ( 7278) SS BOND : bond 0.00361 ( 2) SS BOND : angle 0.26614 ( 4) hydrogen bonds : bond 0.04870 ( 201) hydrogen bonds : angle 5.66801 ( 555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: L 53 SER cc_start: 0.7516 (p) cc_final: 0.7100 (t) REVERT: A 21 TYR cc_start: 0.6249 (m-80) cc_final: 0.5971 (m-10) REVERT: A 35 ASP cc_start: 0.8234 (t0) cc_final: 0.7926 (t0) REVERT: A 105 ILE cc_start: 0.5832 (OUTLIER) cc_final: 0.5354 (mt) REVERT: A 113 TYR cc_start: 0.6879 (m-10) cc_final: 0.6616 (m-10) REVERT: A 249 ASP cc_start: 0.7381 (t70) cc_final: 0.7115 (t0) REVERT: A 275 ASN cc_start: 0.8569 (m-40) cc_final: 0.7932 (m110) REVERT: A 316 SER cc_start: 0.7467 (OUTLIER) cc_final: 0.7140 (p) REVERT: A 337 ARG cc_start: 0.8257 (mtp85) cc_final: 0.8050 (mtp85) REVERT: A 338 GLN cc_start: 0.7927 (tp-100) cc_final: 0.7454 (tp40) outliers start: 26 outliers final: 19 residues processed: 148 average time/residue: 0.0902 time to fit residues: 16.8168 Evaluate side-chains 146 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 24 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133989 restraints weight = 7802.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137908 restraints weight = 4290.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140371 restraints weight = 2800.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.142223 restraints weight = 2074.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143316 restraints weight = 1649.289| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5366 Z= 0.177 Angle : 0.619 8.095 7282 Z= 0.324 Chirality : 0.045 0.161 822 Planarity : 0.004 0.046 932 Dihedral : 5.191 22.868 726 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.73 % Allowed : 22.94 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.66 (0.33), residues: 661 helix: 2.78 (0.54), residues: 95 sheet: -0.33 (0.33), residues: 268 loop : -1.63 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 289 TYR 0.017 0.002 TYR A 54 PHE 0.018 0.002 PHE A 369 TRP 0.009 0.002 TRP H 111 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 5364) covalent geometry : angle 0.61918 ( 7278) SS BOND : bond 0.00367 ( 2) SS BOND : angle 0.27344 ( 4) hydrogen bonds : bond 0.04942 ( 201) hydrogen bonds : angle 5.65993 ( 555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 53 SER cc_start: 0.7563 (p) cc_final: 0.7145 (t) REVERT: A 21 TYR cc_start: 0.6244 (m-80) cc_final: 0.5984 (m-10) REVERT: A 105 ILE cc_start: 0.5891 (OUTLIER) cc_final: 0.5384 (mt) REVERT: A 113 TYR cc_start: 0.6852 (m-10) cc_final: 0.6574 (m-10) REVERT: A 172 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: A 249 ASP cc_start: 0.7349 (t70) cc_final: 0.7095 (t0) REVERT: A 275 ASN cc_start: 0.8556 (m-40) cc_final: 0.8036 (m110) REVERT: A 316 SER cc_start: 0.7448 (OUTLIER) cc_final: 0.7132 (p) REVERT: A 327 LYS cc_start: 0.6528 (mtpt) cc_final: 0.6270 (mtpp) REVERT: A 338 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7418 (tp40) outliers start: 27 outliers final: 20 residues processed: 148 average time/residue: 0.0879 time to fit residues: 16.2182 Evaluate side-chains 152 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 50 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 264 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.156234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.134730 restraints weight = 7657.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138592 restraints weight = 4246.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.141164 restraints weight = 2790.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.142345 restraints weight = 2056.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.143843 restraints weight = 1716.076| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5366 Z= 0.203 Angle : 0.660 8.275 7282 Z= 0.342 Chirality : 0.046 0.171 822 Planarity : 0.004 0.047 932 Dihedral : 5.295 23.285 726 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.90 % Allowed : 23.82 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.75 (0.33), residues: 661 helix: 2.61 (0.53), residues: 95 sheet: -0.36 (0.33), residues: 262 loop : -1.65 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 289 TYR 0.018 0.002 TYR A 422 PHE 0.020 0.002 PHE H 35 TRP 0.009 0.002 TRP H 111 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 5364) covalent geometry : angle 0.65970 ( 7278) SS BOND : bond 0.00384 ( 2) SS BOND : angle 0.31899 ( 4) hydrogen bonds : bond 0.05085 ( 201) hydrogen bonds : angle 5.75337 ( 555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: L 53 SER cc_start: 0.7543 (p) cc_final: 0.7126 (t) REVERT: A 21 TYR cc_start: 0.6265 (m-80) cc_final: 0.5999 (m-10) REVERT: A 105 ILE cc_start: 0.5991 (OUTLIER) cc_final: 0.5472 (mt) REVERT: A 113 TYR cc_start: 0.6854 (m-10) cc_final: 0.6589 (m-10) REVERT: A 316 SER cc_start: 0.7482 (OUTLIER) cc_final: 0.7114 (p) REVERT: A 327 LYS cc_start: 0.6571 (mtpt) cc_final: 0.6293 (mtpp) REVERT: A 338 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7451 (tp40) outliers start: 28 outliers final: 21 residues processed: 138 average time/residue: 0.0921 time to fit residues: 15.9622 Evaluate side-chains 137 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 17 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 264 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.155855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.134565 restraints weight = 7702.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138344 restraints weight = 4222.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140822 restraints weight = 2762.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.142428 restraints weight = 2041.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.143863 restraints weight = 1650.940| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5366 Z= 0.210 Angle : 0.659 8.513 7282 Z= 0.344 Chirality : 0.047 0.171 822 Planarity : 0.005 0.047 932 Dihedral : 5.344 23.569 726 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.55 % Allowed : 24.17 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.72 (0.33), residues: 661 helix: 2.57 (0.52), residues: 95 sheet: -0.34 (0.32), residues: 277 loop : -1.66 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.019 0.002 TYR A 422 PHE 0.019 0.002 PHE H 35 TRP 0.010 0.002 TRP H 111 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 5364) covalent geometry : angle 0.65927 ( 7278) SS BOND : bond 0.00395 ( 2) SS BOND : angle 0.32493 ( 4) hydrogen bonds : bond 0.05185 ( 201) hydrogen bonds : angle 5.77249 ( 555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: L 12 LEU cc_start: 0.8585 (mm) cc_final: 0.8214 (mp) REVERT: L 53 SER cc_start: 0.7640 (p) cc_final: 0.7226 (t) REVERT: A 21 TYR cc_start: 0.6264 (m-80) cc_final: 0.5996 (m-10) REVERT: A 105 ILE cc_start: 0.6015 (OUTLIER) cc_final: 0.5497 (mt) REVERT: A 113 TYR cc_start: 0.6837 (m-10) cc_final: 0.6590 (m-10) REVERT: A 316 SER cc_start: 0.7499 (OUTLIER) cc_final: 0.7119 (p) REVERT: A 327 LYS cc_start: 0.6609 (mtpt) cc_final: 0.6306 (mtpp) REVERT: A 337 ARG cc_start: 0.8261 (mtp85) cc_final: 0.8056 (mtp85) REVERT: A 338 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7432 (tp40) outliers start: 26 outliers final: 23 residues processed: 129 average time/residue: 0.0844 time to fit residues: 13.6876 Evaluate side-chains 135 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 17 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 264 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135137 restraints weight = 7678.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.138922 restraints weight = 4250.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141481 restraints weight = 2790.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.143126 restraints weight = 2052.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144400 restraints weight = 1646.845| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5366 Z= 0.191 Angle : 0.659 8.694 7282 Z= 0.341 Chirality : 0.046 0.168 822 Planarity : 0.004 0.047 932 Dihedral : 5.257 23.158 726 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.20 % Allowed : 24.87 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.70 (0.33), residues: 661 helix: 2.54 (0.52), residues: 95 sheet: -0.32 (0.32), residues: 279 loop : -1.64 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.017 0.002 TYR A 422 PHE 0.019 0.002 PHE H 35 TRP 0.009 0.002 TRP H 111 HIS 0.003 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 5364) covalent geometry : angle 0.65875 ( 7278) SS BOND : bond 0.00367 ( 2) SS BOND : angle 0.29023 ( 4) hydrogen bonds : bond 0.04957 ( 201) hydrogen bonds : angle 5.72728 ( 555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1322 Ramachandran restraints generated. 661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: L 12 LEU cc_start: 0.8586 (mm) cc_final: 0.8205 (mp) REVERT: L 53 SER cc_start: 0.7527 (p) cc_final: 0.7110 (t) REVERT: A 21 TYR cc_start: 0.6243 (m-80) cc_final: 0.5968 (m-10) REVERT: A 105 ILE cc_start: 0.5995 (OUTLIER) cc_final: 0.5284 (mm) REVERT: A 113 TYR cc_start: 0.6794 (m-10) cc_final: 0.6568 (m-10) REVERT: A 316 SER cc_start: 0.7471 (OUTLIER) cc_final: 0.7105 (p) REVERT: A 327 LYS cc_start: 0.6585 (mtpt) cc_final: 0.6261 (mtpp) REVERT: A 337 ARG cc_start: 0.8272 (mtp85) cc_final: 0.8068 (mtp85) REVERT: A 338 GLN cc_start: 0.8011 (tp-100) cc_final: 0.7548 (tp40) outliers start: 24 outliers final: 20 residues processed: 128 average time/residue: 0.0941 time to fit residues: 15.1951 Evaluate side-chains 132 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 444 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 63 optimal weight: 0.0370 chunk 21 optimal weight: 0.3980 chunk 39 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 264 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.159136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137805 restraints weight = 7777.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.141678 restraints weight = 4302.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.144203 restraints weight = 2829.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.145528 restraints weight = 2095.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.147021 restraints weight = 1734.141| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5366 Z= 0.138 Angle : 0.612 8.642 7282 Z= 0.316 Chirality : 0.045 0.159 822 Planarity : 0.004 0.046 932 Dihedral : 4.923 21.645 726 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.20 % Allowed : 24.69 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 aren not related in a simple way. whole: -0.59 (0.33), residues: 661 helix: 2.74 (0.54), residues: 95 sheet: -0.21 (0.33), residues: 264 loop : -1.61 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.016 0.001 TYR A 54 PHE 0.016 0.002 PHE A 369 TRP 0.009 0.002 TRP L 36 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5364) covalent geometry : angle 0.61236 ( 7278) SS BOND : bond 0.00327 ( 2) SS BOND : angle 0.30770 ( 4) hydrogen bonds : bond 0.04427 ( 201) hydrogen bonds : angle 5.52011 ( 555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1138.17 seconds wall clock time: 20 minutes 21.78 seconds (1221.78 seconds total)