Starting phenix.real_space_refine on Sat May 10 05:49:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dng_47040/05_2025/9dng_47040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dng_47040/05_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_47040/05_2025/9dng_47040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dng_47040/05_2025/9dng_47040.map" model { file = "/net/cci-nas-00/data/ceres_data/9dng_47040/05_2025/9dng_47040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dng_47040/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 3.85, per 1000 atoms: 0.73 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: 1.23 Conformation dependent library (CDL) restraints added in 647.2 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: 0.68 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: 1.65 Time building geometry restraints manager: 1.46 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: 0.010 Normalize map: mean=0, sd=1: 1.710 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.320 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.830 ------------------------------------------------------------------------------- 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 : 7.46 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 Details of bonding type rmsd hydrogen bonds : bond 0.23897 ( 201) hydrogen bonds : angle 8.96349 ( 555) SS BOND : bond 0.00361 ( 2) SS BOND : angle 0.27921 ( 4) covalent geometry : bond 0.00337 ( 5364) covalent geometry : angle 0.63251 ( 7278) *********************** 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 : 0.549 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: 0.1948 time to fit residues: 31.1437 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 : 0.582 ------------------------------------------------------------------------------- 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: 0.9990 chunk 20 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 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 = 7631.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136581 restraints weight = 4522.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.138971 restraints weight = 3113.663| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 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 5366 Z= 0.146 Angle : 0.611 6.954 7282 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 Details of bonding type rmsd hydrogen bonds : bond 0.05399 ( 201) hydrogen bonds : angle 6.32519 ( 555) SS BOND : bond 0.00339 ( 2) SS BOND : angle 0.22271 ( 4) covalent geometry : bond 0.00323 ( 5364) covalent geometry : angle 0.61117 ( 7278) *********************** 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 : 0.657 Fit side-chains REVERT: A 184 GLU cc_start: 0.7007 (tp30) cc_final: 0.6025 (tp30) REVERT: A 275 ASN cc_start: 0.8490 (m-40) cc_final: 0.7896 (m110) REVERT: A 316 SER cc_start: 0.7459 (OUTLIER) cc_final: 0.7119 (p) REVERT: A 338 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7836 (tp40) outliers start: 11 outliers final: 4 residues processed: 127 average time/residue: 0.1977 time to fit residues: 31.6467 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 : 0.639 ------------------------------------------------------------------------------- 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: 0.0000 chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 57 optimal weight: 0.0980 overall best weight: 0.2742 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.158397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136579 restraints weight = 7744.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140303 restraints weight = 4269.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143006 restraints weight = 2833.055| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1254 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= 0.140 Angle : 0.591 7.612 7282 Z= 0.308 Chirality : 0.045 0.147 822 Planarity : 0.004 0.043 932 Dihedral : 4.925 23.782 726 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.33 % Allowed : 22.07 % Favored : 74.61 % 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: -0.51 (0.34), residues: 661 helix: 2.91 (0.56), residues: 95 sheet: -0.13 (0.33), residues: 266 loop : -1.64 (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 0.023 0.002 PHE A 369 TYR 0.020 0.002 TYR A 54 ARG 0.003 0.000 ARG A 289 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 201) hydrogen bonds : angle 5.71051 ( 555) SS BOND : bond 0.00370 ( 2) SS BOND : angle 0.17821 ( 4) covalent geometry : bond 0.00312 ( 5364) covalent geometry : angle 0.59117 ( 7278) *********************** 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 144 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.6348 (t70) cc_final: 0.5943 (t0) REVERT: A 105 ILE cc_start: 0.5814 (OUTLIER) cc_final: 0.5381 (mt) REVERT: A 113 TYR cc_start: 0.6726 (m-10) cc_final: 0.6490 (m-10) REVERT: A 188 ASP cc_start: 0.6440 (m-30) cc_final: 0.6232 (m-30) REVERT: A 275 ASN cc_start: 0.8509 (m-40) cc_final: 0.7955 (m110) REVERT: A 287 THR cc_start: 0.8093 (p) cc_final: 0.7815 (p) REVERT: A 289 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.7016 (ttm-80) REVERT: A 316 SER cc_start: 0.7391 (OUTLIER) cc_final: 0.7100 (p) REVERT: A 338 GLN cc_start: 0.8003 (tp-100) cc_final: 0.7686 (tp40) REVERT: A 357 GLU cc_start: 0.7508 (tp30) cc_final: 0.7124 (tp30) outliers start: 19 outliers final: 10 residues processed: 138 average time/residue: 0.2058 time to fit residues: 35.2836 Evaluate side-chains 136 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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: 0.9990 chunk 29 optimal weight: 0.0770 chunk 20 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 0.0170 chunk 60 optimal weight: 0.9990 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN A 172 GLN A 247 GLN A 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.158906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136982 restraints weight = 7856.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.140702 restraints weight = 4314.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143489 restraints weight = 2855.374| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5366 Z= 0.127 Angle : 0.578 8.117 7282 Z= 0.300 Chirality : 0.044 0.142 822 Planarity : 0.004 0.043 932 Dihedral : 4.768 22.167 726 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.03 % Allowed : 20.84 % 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: -0.41 (0.34), residues: 661 helix: 2.96 (0.55), residues: 95 sheet: -0.03 (0.33), residues: 266 loop : -1.60 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 105 HIS 0.002 0.001 HIS A 159 PHE 0.020 0.002 PHE A 369 TYR 0.017 0.001 TYR A 54 ARG 0.002 0.000 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 201) hydrogen bonds : angle 5.44652 ( 555) SS BOND : bond 0.00359 ( 2) SS BOND : angle 0.19519 ( 4) covalent geometry : bond 0.00282 ( 5364) covalent geometry : angle 0.57790 ( 7278) *********************** 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 151 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: L 104 THR cc_start: 0.7981 (p) cc_final: 0.7556 (t) REVERT: A 105 ILE cc_start: 0.5834 (OUTLIER) cc_final: 0.5386 (mt) REVERT: A 188 ASP cc_start: 0.6476 (m-30) cc_final: 0.6266 (m-30) REVERT: A 275 ASN cc_start: 0.8506 (m-40) cc_final: 0.7950 (m110) REVERT: A 287 THR cc_start: 0.8051 (p) cc_final: 0.7773 (p) REVERT: A 316 SER cc_start: 0.7431 (OUTLIER) cc_final: 0.7180 (p) REVERT: A 338 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7607 (tp40) outliers start: 23 outliers final: 13 residues processed: 144 average time/residue: 0.1824 time to fit residues: 33.0702 Evaluate side-chains 139 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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 406 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 0.0970 chunk 17 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.157175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135502 restraints weight = 7678.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139049 restraints weight = 4246.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141929 restraints weight = 2847.417| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5366 Z= 0.143 Angle : 0.582 8.581 7282 Z= 0.302 Chirality : 0.044 0.143 822 Planarity : 0.004 0.043 932 Dihedral : 4.823 22.440 726 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.03 % Allowed : 21.02 % 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: -0.39 (0.34), residues: 661 helix: 2.97 (0.55), residues: 95 sheet: -0.02 (0.33), residues: 264 loop : -1.58 (0.34), residues: 302 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 0.019 0.002 PHE A 369 TYR 0.016 0.001 TYR A 54 ARG 0.002 0.000 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 201) hydrogen bonds : angle 5.35313 ( 555) SS BOND : bond 0.00369 ( 2) SS BOND : angle 0.22429 ( 4) covalent geometry : bond 0.00321 ( 5364) covalent geometry : angle 0.58229 ( 7278) *********************** 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 150 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 104 THR cc_start: 0.7972 (p) cc_final: 0.7554 (t) REVERT: A 35 ASP cc_start: 0.8161 (t0) cc_final: 0.7904 (t0) REVERT: A 105 ILE cc_start: 0.5886 (OUTLIER) cc_final: 0.5433 (mt) REVERT: A 249 ASP cc_start: 0.7408 (t70) cc_final: 0.7163 (t0) REVERT: A 275 ASN cc_start: 0.8464 (m-40) cc_final: 0.7929 (m110) REVERT: A 316 SER cc_start: 0.7411 (OUTLIER) cc_final: 0.7093 (p) REVERT: A 338 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7530 (tp40) outliers start: 23 outliers final: 17 residues processed: 144 average time/residue: 0.2061 time to fit residues: 37.0763 Evaluate side-chains 145 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 4 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 21 optimal weight: 0.2980 chunk 54 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 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 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 = 0.3928 r_free = 0.3928 target = 0.156849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135235 restraints weight = 7658.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139139 restraints weight = 4236.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141769 restraints weight = 2774.093| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.1723 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= 0.186 Angle : 0.619 8.634 7282 Z= 0.323 Chirality : 0.045 0.153 822 Planarity : 0.004 0.045 932 Dihedral : 5.108 22.791 726 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.38 % Allowed : 21.37 % 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 (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: -0.51 (0.34), residues: 661 helix: 2.77 (0.54), residues: 95 sheet: -0.17 (0.33), residues: 268 loop : -1.55 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 117 HIS 0.003 0.001 HIS A 159 PHE 0.018 0.002 PHE A 369 TYR 0.019 0.002 TYR A 422 ARG 0.002 0.000 ARG A 289 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 201) hydrogen bonds : angle 5.53761 ( 555) SS BOND : bond 0.00391 ( 2) SS BOND : angle 0.25972 ( 4) covalent geometry : bond 0.00424 ( 5364) covalent geometry : angle 0.61886 ( 7278) *********************** 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 154 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: L 53 SER cc_start: 0.7504 (p) cc_final: 0.7060 (t) REVERT: L 104 THR cc_start: 0.7952 (p) cc_final: 0.7509 (t) REVERT: A 35 ASP cc_start: 0.8213 (t0) cc_final: 0.7939 (t0) REVERT: A 105 ILE cc_start: 0.6013 (OUTLIER) cc_final: 0.5558 (mt) REVERT: A 113 TYR cc_start: 0.6921 (m-10) cc_final: 0.6629 (m-10) REVERT: A 249 ASP cc_start: 0.7394 (t70) cc_final: 0.7147 (t0) REVERT: A 275 ASN cc_start: 0.8472 (m-40) cc_final: 0.7881 (m110) REVERT: A 316 SER cc_start: 0.7394 (OUTLIER) cc_final: 0.7084 (p) REVERT: A 327 LYS cc_start: 0.6208 (mtpt) cc_final: 0.5857 (mtpp) REVERT: A 338 GLN cc_start: 0.7983 (tp-100) cc_final: 0.7516 (tp40) outliers start: 25 outliers final: 17 residues processed: 144 average time/residue: 0.1911 time to fit residues: 34.4654 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 : 0.623 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.154466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132998 restraints weight = 7621.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136828 restraints weight = 4211.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139279 restraints weight = 2760.676| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 5366 Z= 0.288 Angle : 0.711 8.799 7282 Z= 0.375 Chirality : 0.048 0.176 822 Planarity : 0.005 0.048 932 Dihedral : 5.728 25.912 726 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.55 % Allowed : 22.07 % Favored : 73.38 % 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: -0.77 (0.33), residues: 661 helix: 2.41 (0.54), residues: 95 sheet: -0.34 (0.32), residues: 278 loop : -1.69 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP H 117 HIS 0.005 0.001 HIS A 159 PHE 0.023 0.003 PHE A 149 TYR 0.024 0.002 TYR A 422 ARG 0.005 0.001 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.05998 ( 201) hydrogen bonds : angle 6.02367 ( 555) SS BOND : bond 0.00436 ( 2) SS BOND : angle 0.43273 ( 4) covalent geometry : bond 0.00658 ( 5364) covalent geometry : angle 0.71106 ( 7278) *********************** 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 151 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: L 5 MET cc_start: 0.7540 (mmp) cc_final: 0.7186 (mmm) REVERT: L 53 SER cc_start: 0.7699 (p) cc_final: 0.7293 (t) REVERT: A 35 ASP cc_start: 0.8298 (t0) cc_final: 0.7999 (t0) REVERT: A 105 ILE cc_start: 0.6058 (OUTLIER) cc_final: 0.5547 (mt) REVERT: A 113 TYR cc_start: 0.6929 (m-10) cc_final: 0.6627 (m-10) REVERT: A 153 ASN cc_start: 0.7059 (m-40) cc_final: 0.6684 (m-40) REVERT: A 249 ASP cc_start: 0.7463 (t70) cc_final: 0.7228 (t0) REVERT: A 316 SER cc_start: 0.7410 (OUTLIER) cc_final: 0.7081 (p) REVERT: A 338 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7477 (tp40) outliers start: 26 outliers final: 19 residues processed: 143 average time/residue: 0.1915 time to fit residues: 34.2834 Evaluate side-chains 142 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 298 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 306 LYS 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: 0.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 65 optimal weight: 0.0170 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 0.0470 chunk 3 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.157023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.135504 restraints weight = 7696.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139196 restraints weight = 4231.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141835 restraints weight = 2807.627| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5366 Z= 0.159 Angle : 0.625 8.769 7282 Z= 0.326 Chirality : 0.045 0.166 822 Planarity : 0.004 0.046 932 Dihedral : 5.222 23.897 726 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.03 % Allowed : 23.47 % Favored : 72.50 % 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: -0.60 (0.34), residues: 661 helix: 2.62 (0.53), residues: 95 sheet: -0.19 (0.32), residues: 279 loop : -1.66 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 111 HIS 0.002 0.001 HIS A 111 PHE 0.019 0.002 PHE A 369 TYR 0.014 0.002 TYR A 422 ARG 0.002 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 201) hydrogen bonds : angle 5.73421 ( 555) SS BOND : bond 0.00392 ( 2) SS BOND : angle 0.26095 ( 4) covalent geometry : bond 0.00361 ( 5364) covalent geometry : angle 0.62473 ( 7278) *********************** 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: 23 poor density : 120 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: L 5 MET cc_start: 0.7501 (mmp) cc_final: 0.7168 (mmm) REVERT: L 53 SER cc_start: 0.7505 (p) cc_final: 0.7086 (t) REVERT: A 35 ASP cc_start: 0.8301 (t0) cc_final: 0.7958 (t0) REVERT: A 105 ILE cc_start: 0.6015 (OUTLIER) cc_final: 0.5381 (mm) REVERT: A 113 TYR cc_start: 0.6829 (m-10) cc_final: 0.6604 (m-10) REVERT: A 249 ASP cc_start: 0.7347 (t70) cc_final: 0.7117 (t0) REVERT: A 286 GLU cc_start: 0.6677 (mp0) cc_final: 0.6476 (mp0) REVERT: A 316 SER cc_start: 0.7382 (OUTLIER) cc_final: 0.7020 (p) REVERT: A 327 LYS cc_start: 0.6624 (mtpt) cc_final: 0.6357 (mtpp) REVERT: A 338 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7475 (tp40) outliers start: 23 outliers final: 18 residues processed: 135 average time/residue: 0.1941 time to fit residues: 32.7915 Evaluate side-chains 144 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 20 optimal weight: 0.0980 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 chunk 30 optimal weight: 0.0170 chunk 36 optimal weight: 0.0040 chunk 29 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.1430 ------------------------------------------------------------------------------- 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 400 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.160894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139625 restraints weight = 7640.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143412 restraints weight = 4289.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145969 restraints weight = 2854.305| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5366 Z= 0.112 Angle : 0.583 8.632 7282 Z= 0.301 Chirality : 0.044 0.150 822 Planarity : 0.004 0.044 932 Dihedral : 4.726 21.726 726 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.33 % Allowed : 24.87 % Favored : 71.80 % 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: -0.32 (0.34), residues: 661 helix: 2.89 (0.55), residues: 95 sheet: -0.04 (0.32), residues: 277 loop : -1.46 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 36 HIS 0.002 0.000 HIS A 454 PHE 0.017 0.002 PHE H 35 TYR 0.012 0.001 TYR A 54 ARG 0.004 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 201) hydrogen bonds : angle 5.30693 ( 555) SS BOND : bond 0.00343 ( 2) SS BOND : angle 0.25496 ( 4) covalent geometry : bond 0.00248 ( 5364) covalent geometry : angle 0.58322 ( 7278) *********************** 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 137 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: H 8 VAL cc_start: 0.7752 (t) cc_final: 0.7469 (m) REVERT: L 53 SER cc_start: 0.7371 (p) cc_final: 0.6966 (t) REVERT: A 105 ILE cc_start: 0.5995 (OUTLIER) cc_final: 0.5358 (mm) REVERT: A 316 SER cc_start: 0.7332 (OUTLIER) cc_final: 0.7082 (p) REVERT: A 327 LYS cc_start: 0.6576 (mtpt) cc_final: 0.6309 (mtpp) REVERT: A 338 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7605 (tp40) outliers start: 19 outliers final: 12 residues processed: 130 average time/residue: 0.1971 time to fit residues: 32.5415 Evaluate side-chains 136 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS 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 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: 0.7980 chunk 46 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN A 189 ASN A 247 GLN A 264 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.155475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134104 restraints weight = 7718.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.137888 restraints weight = 4279.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.140464 restraints weight = 2816.375| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5366 Z= 0.236 Angle : 0.675 8.351 7282 Z= 0.353 Chirality : 0.047 0.172 822 Planarity : 0.005 0.047 932 Dihedral : 5.288 23.999 726 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.33 % Allowed : 25.74 % 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 (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: -0.57 (0.34), residues: 661 helix: 2.64 (0.54), residues: 95 sheet: -0.15 (0.32), residues: 277 loop : -1.66 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 117 HIS 0.006 0.001 HIS H 38 PHE 0.020 0.003 PHE H 35 TYR 0.022 0.002 TYR A 422 ARG 0.004 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.05295 ( 201) hydrogen bonds : angle 5.74416 ( 555) SS BOND : bond 0.00387 ( 2) SS BOND : angle 0.34600 ( 4) covalent geometry : bond 0.00543 ( 5364) covalent geometry : angle 0.67515 ( 7278) ********************** 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 137 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.171 Fit side-chains REVERT: L 5 MET cc_start: 0.7501 (mmp) cc_final: 0.7180 (mmm) REVERT: L 53 SER cc_start: 0.7564 (p) cc_final: 0.7163 (t) REVERT: A 35 ASP cc_start: 0.8237 (t0) cc_final: 0.7880 (t0) REVERT: A 105 ILE cc_start: 0.6014 (OUTLIER) cc_final: 0.5292 (mm) REVERT: A 184 GLU cc_start: 0.7029 (tp30) cc_final: 0.6109 (tp30) REVERT: A 316 SER cc_start: 0.7362 (OUTLIER) cc_final: 0.7006 (p) REVERT: A 338 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7477 (tp40) outliers start: 19 outliers final: 14 residues processed: 131 average time/residue: 0.2068 time to fit residues: 34.0850 Evaluate side-chains 134 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 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 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 444 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.155722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.134451 restraints weight = 7709.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138236 restraints weight = 4262.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.140796 restraints weight = 2795.221| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5366 Z= 0.230 Angle : 0.675 8.304 7282 Z= 0.352 Chirality : 0.047 0.173 822 Planarity : 0.005 0.046 932 Dihedral : 5.369 23.752 726 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.98 % Allowed : 25.74 % 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 (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: 2.47 (0.54), residues: 95 sheet: -0.25 (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 0.019 0.003 PHE H 35 TYR 0.020 0.002 TYR A 422 ARG 0.003 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.05317 ( 201) hydrogen bonds : angle 5.82085 ( 555) SS BOND : bond 0.00431 ( 2) SS BOND : angle 0.39465 ( 4) covalent geometry : bond 0.00527 ( 5364) covalent geometry : angle 0.67547 ( 7278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2128.12 seconds wall clock time: 37 minutes 56.81 seconds (2276.81 seconds total)