Starting phenix.real_space_refine on Thu Mar 6 07:09:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dng_47040/03_2025/9dng_47040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dng_47040/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dng_47040/03_2025/9dng_47040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dng_47040/03_2025/9dng_47040.map" model { file = "/net/cci-nas-00/data/ceres_data/9dng_47040/03_2025/9dng_47040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dng_47040/03_2025/9dng_47040.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 3.75, per 1000 atoms: 0.71 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: 1.17 Conformation dependent library (CDL) restraints added in 627.6 milliseconds 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: 0.69 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: 1.62 Time building geometry restraints manager: 1.41 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.370 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.690 ------------------------------------------------------------------------------- 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 5364 Z= 0.217 Angle : 0.633 9.635 7278 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 : 7.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP H 111 HIS 0.002 0.001 HIS A 311 PHE 0.016 0.002 PHE A 369 TYR 0.015 0.002 TYR A 54 ARG 0.007 0.000 ARG A 289 *********************** 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 : 0.539 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: 0.1913 time to fit residues: 30.6122 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 : 0.602 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 0.0770 chunk 17 optimal weight: 0.0270 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.156243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132960 restraints weight = 7631.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136584 restraints weight = 4522.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.139202 restraints weight = 3112.035| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5364 Z= 0.208 Angle : 0.611 6.954 7278 Z= 0.323 Chirality : 0.045 0.156 822 Planarity : 0.004 0.042 932 Dihedral : 5.184 29.290 728 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.93 % Allowed : 20.84 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.34), residues: 661 helix: 2.89 (0.56), residues: 95 sheet: -0.25 (0.33), residues: 271 loop : -1.59 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 36 HIS 0.002 0.001 HIS A 159 PHE 0.027 0.002 PHE A 369 TYR 0.025 0.002 TYR A 54 ARG 0.005 0.000 ARG A 289 *********************** 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 132 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.547 Fit side-chains REVERT: A 184 GLU cc_start: 0.6990 (tp30) cc_final: 0.6016 (tp30) REVERT: A 275 ASN cc_start: 0.8488 (m-40) cc_final: 0.7896 (m110) REVERT: A 316 SER cc_start: 0.7461 (OUTLIER) cc_final: 0.7121 (p) REVERT: A 338 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7838 (tp40) outliers start: 11 outliers final: 4 residues processed: 127 average time/residue: 0.1971 time to fit residues: 31.6272 Evaluate side-chains 119 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 35 optimal weight: 0.9980 chunk 32 optimal weight: 0.0070 chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 53 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.0980 overall best weight: 0.3398 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.157680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135918 restraints weight = 7726.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139484 restraints weight = 4254.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.142191 restraints weight = 2845.591| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5364 Z= 0.233 Angle : 0.606 7.596 7278 Z= 0.317 Chirality : 0.045 0.150 822 Planarity : 0.004 0.044 932 Dihedral : 5.038 24.093 726 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.15 % Allowed : 21.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.34), residues: 661 helix: 2.89 (0.55), residues: 95 sheet: -0.24 (0.33), residues: 264 loop : -1.62 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 105 HIS 0.003 0.001 HIS A 159 PHE 0.023 0.002 PHE A 369 TYR 0.020 0.002 TYR A 54 ARG 0.004 0.000 ARG A 289 *********************** 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 145 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.6326 (t70) cc_final: 0.5919 (t0) REVERT: A 105 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.5430 (mt) REVERT: A 184 GLU cc_start: 0.7044 (tp30) cc_final: 0.5771 (tp30) REVERT: A 188 ASP cc_start: 0.6473 (m-30) cc_final: 0.4807 (m-30) REVERT: A 275 ASN cc_start: 0.8516 (m-40) cc_final: 0.7975 (m110) REVERT: A 287 THR cc_start: 0.8108 (p) cc_final: 0.7817 (p) REVERT: A 289 ARG cc_start: 0.7472 (ttm-80) cc_final: 0.7027 (ttm-80) REVERT: A 316 SER cc_start: 0.7395 (OUTLIER) cc_final: 0.7175 (p) REVERT: A 338 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7668 (tp40) REVERT: A 357 GLU cc_start: 0.7545 (tp30) cc_final: 0.7158 (tp30) outliers start: 18 outliers final: 10 residues processed: 139 average time/residue: 0.2135 time to fit residues: 37.0199 Evaluate side-chains 137 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 54 optimal weight: 0.8980 chunk 29 optimal weight: 0.0370 chunk 20 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 31 optimal weight: 0.0470 chunk 36 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 overall best weight: 0.2956 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.157986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136249 restraints weight = 7817.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140020 restraints weight = 4276.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.142530 restraints weight = 2819.818| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5364 Z= 0.210 Angle : 0.594 7.909 7278 Z= 0.309 Chirality : 0.044 0.146 822 Planarity : 0.004 0.043 932 Dihedral : 4.909 22.471 726 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.38 % Allowed : 20.67 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.34), residues: 661 helix: 2.89 (0.55), residues: 95 sheet: -0.12 (0.33), residues: 266 loop : -1.63 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 105 HIS 0.002 0.001 HIS A 159 PHE 0.021 0.002 PHE A 369 TYR 0.018 0.002 TYR A 54 ARG 0.002 0.000 ARG A 289 *********************** 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 156 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 104 THR cc_start: 0.7988 (p) cc_final: 0.7550 (t) REVERT: A 29 ASP cc_start: 0.6371 (t70) cc_final: 0.6010 (t0) REVERT: A 105 ILE cc_start: 0.5891 (OUTLIER) cc_final: 0.5438 (mt) REVERT: A 188 ASP cc_start: 0.6517 (m-30) cc_final: 0.6287 (m-30) REVERT: A 275 ASN cc_start: 0.8516 (m-40) cc_final: 0.7950 (m110) REVERT: A 287 THR cc_start: 0.8077 (p) cc_final: 0.7800 (p) REVERT: A 316 SER cc_start: 0.7423 (OUTLIER) cc_final: 0.7167 (p) REVERT: A 338 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7616 (tp40) outliers start: 25 outliers final: 16 residues processed: 148 average time/residue: 0.1971 time to fit residues: 36.5857 Evaluate side-chains 143 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 374 THR Chi-restraints excluded: chain A residue 406 LEU 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 53 optimal weight: 0.0570 chunk 17 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.0570 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN 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 = 0.3927 r_free = 0.3927 target = 0.156863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135157 restraints weight = 7688.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.138883 restraints weight = 4267.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141594 restraints weight = 2828.138| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5364 Z= 0.212 Angle : 0.584 8.234 7278 Z= 0.304 Chirality : 0.044 0.146 822 Planarity : 0.004 0.043 932 Dihedral : 4.883 22.613 726 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.38 % Allowed : 20.84 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.34), residues: 661 helix: 2.98 (0.56), residues: 95 sheet: -0.08 (0.33), residues: 264 loop : -1.63 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 105 HIS 0.002 0.001 HIS A 159 PHE 0.020 0.002 PHE A 369 TYR 0.016 0.002 TYR A 54 ARG 0.002 0.000 ARG A 432 *********************** 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 154 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 53 SER cc_start: 0.7462 (p) cc_final: 0.7033 (t) REVERT: L 104 THR cc_start: 0.7958 (p) cc_final: 0.7530 (t) REVERT: A 35 ASP cc_start: 0.8187 (t0) cc_final: 0.7904 (t0) REVERT: A 105 ILE cc_start: 0.5901 (OUTLIER) cc_final: 0.5450 (mt) REVERT: A 275 ASN cc_start: 0.8527 (m-40) cc_final: 0.7970 (m110) REVERT: A 316 SER cc_start: 0.7396 (OUTLIER) cc_final: 0.7085 (p) REVERT: A 338 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7465 (tp40) outliers start: 25 outliers final: 16 residues processed: 147 average time/residue: 0.2057 time to fit residues: 37.7591 Evaluate side-chains 145 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 21 optimal weight: 0.1980 chunk 54 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.156712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135017 restraints weight = 7666.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138883 restraints weight = 4254.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141502 restraints weight = 2802.075| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5364 Z= 0.239 Angle : 0.598 8.405 7278 Z= 0.312 Chirality : 0.045 0.147 822 Planarity : 0.004 0.044 932 Dihedral : 4.945 22.116 726 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.85 % Allowed : 22.24 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.33), residues: 661 helix: 2.87 (0.55), residues: 95 sheet: -0.09 (0.33), residues: 264 loop : -1.59 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 111 HIS 0.002 0.001 HIS A 159 PHE 0.018 0.002 PHE A 369 TYR 0.016 0.002 TYR A 422 ARG 0.002 0.000 ARG A 289 *********************** 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 149 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: L 104 THR cc_start: 0.7946 (p) cc_final: 0.7527 (t) REVERT: A 35 ASP cc_start: 0.8207 (t0) cc_final: 0.7968 (t0) REVERT: A 105 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5491 (mt) REVERT: A 113 TYR cc_start: 0.6879 (m-10) cc_final: 0.6568 (m-10) REVERT: A 275 ASN cc_start: 0.8478 (m-40) cc_final: 0.7864 (m110) REVERT: A 316 SER cc_start: 0.7425 (OUTLIER) cc_final: 0.7107 (p) REVERT: A 327 LYS cc_start: 0.6707 (mtpt) cc_final: 0.6256 (mtpp) REVERT: A 338 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7444 (tp40) outliers start: 22 outliers final: 17 residues processed: 141 average time/residue: 0.1920 time to fit residues: 33.8650 Evaluate side-chains 151 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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 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 49 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 55 optimal weight: 0.3980 chunk 42 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.155590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134057 restraints weight = 7630.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137971 restraints weight = 4208.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.139764 restraints weight = 2747.370| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5364 Z= 0.351 Angle : 0.656 8.850 7278 Z= 0.345 Chirality : 0.046 0.159 822 Planarity : 0.005 0.047 932 Dihedral : 5.383 24.307 726 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.55 % Allowed : 22.59 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.33), residues: 661 helix: 2.68 (0.54), residues: 95 sheet: -0.33 (0.33), residues: 269 loop : -1.54 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 117 HIS 0.004 0.001 HIS A 159 PHE 0.021 0.003 PHE H 35 TYR 0.021 0.002 TYR A 422 ARG 0.004 0.000 ARG A 337 *********************** 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 155 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: L 5 MET cc_start: 0.7537 (mmp) cc_final: 0.7187 (mmm) REVERT: L 53 SER cc_start: 0.7596 (p) cc_final: 0.7187 (t) REVERT: A 35 ASP cc_start: 0.8293 (t0) cc_final: 0.7914 (t0) REVERT: A 105 ILE cc_start: 0.6134 (OUTLIER) cc_final: 0.5655 (mt) REVERT: A 113 TYR cc_start: 0.6912 (m-10) cc_final: 0.6623 (m-10) REVERT: A 275 ASN cc_start: 0.8524 (m-40) cc_final: 0.8014 (m110) REVERT: A 316 SER cc_start: 0.7413 (OUTLIER) cc_final: 0.7094 (p) REVERT: A 327 LYS cc_start: 0.6856 (mtpt) cc_final: 0.6460 (mtpt) REVERT: A 338 GLN cc_start: 0.8049 (tp-100) cc_final: 0.7505 (tp40) outliers start: 26 outliers final: 18 residues processed: 147 average time/residue: 0.1992 time to fit residues: 36.7007 Evaluate side-chains 147 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 105 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 35 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN A 247 GLN A 264 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134067 restraints weight = 7703.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137970 restraints weight = 4241.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.140511 restraints weight = 2776.700| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5364 Z= 0.348 Angle : 0.666 8.364 7278 Z= 0.350 Chirality : 0.047 0.158 822 Planarity : 0.005 0.047 932 Dihedral : 5.510 24.958 726 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.20 % Allowed : 23.64 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.34), residues: 661 helix: 2.62 (0.54), residues: 95 sheet: -0.29 (0.32), residues: 277 loop : -1.69 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 117 HIS 0.003 0.001 HIS A 111 PHE 0.021 0.003 PHE H 35 TYR 0.021 0.002 TYR A 422 ARG 0.005 0.000 ARG A 337 *********************** 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 143 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: L 5 MET cc_start: 0.7512 (mmp) cc_final: 0.7147 (mmm) REVERT: L 53 SER cc_start: 0.7585 (p) cc_final: 0.7180 (t) REVERT: A 105 ILE cc_start: 0.6129 (OUTLIER) cc_final: 0.5686 (mt) REVERT: A 113 TYR cc_start: 0.6900 (m-10) cc_final: 0.6608 (m-10) REVERT: A 316 SER cc_start: 0.7459 (OUTLIER) cc_final: 0.7134 (p) REVERT: A 327 LYS cc_start: 0.6816 (mtpt) cc_final: 0.6500 (mtpt) REVERT: A 338 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7438 (tp40) outliers start: 24 outliers final: 19 residues processed: 135 average time/residue: 0.1924 time to fit residues: 32.6423 Evaluate side-chains 137 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 0.0000 chunk 60 optimal weight: 0.0000 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 29 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 overall best weight: 0.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 247 GLN A 264 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.162270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140944 restraints weight = 7644.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.144821 restraints weight = 4271.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.147168 restraints weight = 2821.526| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5364 Z= 0.155 Angle : 0.583 8.934 7278 Z= 0.299 Chirality : 0.044 0.146 822 Planarity : 0.004 0.044 932 Dihedral : 4.712 21.057 726 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.50 % Allowed : 24.52 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.34), residues: 661 helix: 2.88 (0.55), residues: 95 sheet: -0.04 (0.33), residues: 277 loop : -1.48 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 36 HIS 0.001 0.000 HIS A 299 PHE 0.015 0.001 PHE A 369 TYR 0.013 0.001 TYR A 54 ARG 0.004 0.000 ARG A 432 *********************** 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 132 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: H 8 VAL cc_start: 0.7756 (t) cc_final: 0.7472 (m) REVERT: A 105 ILE cc_start: 0.5739 (OUTLIER) cc_final: 0.5113 (mm) REVERT: A 286 GLU cc_start: 0.6640 (mp0) cc_final: 0.6434 (mp0) REVERT: A 316 SER cc_start: 0.7424 (OUTLIER) cc_final: 0.7100 (p) REVERT: A 327 LYS cc_start: 0.6667 (mtpt) cc_final: 0.6249 (mtpp) REVERT: A 338 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7612 (tp40) outliers start: 20 outliers final: 13 residues processed: 123 average time/residue: 0.2000 time to fit residues: 30.9224 Evaluate side-chains 122 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain A residue 171 VAL 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 406 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 4 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.156123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134571 restraints weight = 7723.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138394 restraints weight = 4268.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141027 restraints weight = 2814.187| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5364 Z= 0.357 Angle : 0.672 8.653 7278 Z= 0.350 Chirality : 0.047 0.172 822 Planarity : 0.005 0.047 932 Dihedral : 5.315 24.274 726 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.68 % Allowed : 26.09 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.34), residues: 661 helix: 2.80 (0.55), residues: 95 sheet: -0.02 (0.33), residues: 269 loop : -1.71 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 117 HIS 0.005 0.001 HIS H 38 PHE 0.021 0.003 PHE H 35 TYR 0.022 0.002 TYR A 422 ARG 0.007 0.000 ARG A 337 ********************** 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 140 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: L 5 MET cc_start: 0.7503 (mmp) cc_final: 0.7160 (mmm) REVERT: L 53 SER cc_start: 0.7571 (p) cc_final: 0.7144 (t) REVERT: A 105 ILE cc_start: 0.5853 (OUTLIER) cc_final: 0.5192 (mm) REVERT: A 153 ASN cc_start: 0.6991 (m-40) cc_final: 0.6556 (m-40) REVERT: A 316 SER cc_start: 0.7542 (OUTLIER) cc_final: 0.7176 (p) REVERT: A 327 LYS cc_start: 0.6740 (mtpt) cc_final: 0.6202 (mtpp) REVERT: A 338 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7445 (tp40) outliers start: 21 outliers final: 16 residues processed: 133 average time/residue: 0.2001 time to fit residues: 33.3778 Evaluate side-chains 135 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 105 ILE 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 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 400 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 16 optimal weight: 0.1980 chunk 3 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 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 = 0.3933 r_free = 0.3933 target = 0.157144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135656 restraints weight = 7726.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139377 restraints weight = 4299.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.142096 restraints weight = 2852.606| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5364 Z= 0.284 Angle : 0.648 8.688 7278 Z= 0.337 Chirality : 0.046 0.168 822 Planarity : 0.005 0.046 932 Dihedral : 5.237 23.585 726 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.33 % Allowed : 26.27 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.34), residues: 661 helix: 2.66 (0.54), residues: 95 sheet: -0.07 (0.32), residues: 269 loop : -1.70 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 117 HIS 0.003 0.001 HIS A 111 PHE 0.017 0.002 PHE A 80 TYR 0.017 0.002 TYR A 422 ARG 0.005 0.000 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2114.00 seconds wall clock time: 37 minutes 31.99 seconds (2251.99 seconds total)