Starting phenix.real_space_refine on Tue Aug 4 13:56:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ucp_64050/08_2026/9ucp_64050_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ucp_64050/08_2026/9ucp_64050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ucp_64050/08_2026/9ucp_64050_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ucp_64050/08_2026/9ucp_64050_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ucp_64050/08_2026/9ucp_64050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ucp_64050/08_2026/9ucp_64050.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.079 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 20 5.16 5 C 2265 2.51 5 N 598 2.21 5 O 646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3529 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2601 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 13, 'TRANS': 359} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 474 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 8, 'PHE:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 216 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 698 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 4, 'ARG:plan': 4, 'PHE:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 149 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'IXO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.20, per 1000 atoms: 0.34 Number of scatterers: 3529 At special positions: 0 Unit cell: (53.0425, 63.8675, 122.322, 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 20 16.00 O 646 8.00 N 598 7.00 C 2265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 159.5 milliseconds 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 3 sheets defined 69.1% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 24 through 53 removed outlier: 4.230A pdb=" N PHE A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 61 through 88 removed outlier: 4.501A pdb=" N MET A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASN A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 129 removed outlier: 4.079A pdb=" N ALA A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.704A pdb=" N ARG A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 168 removed outlier: 3.527A pdb=" N SER A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.358A pdb=" N GLN A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 197 through 232 removed outlier: 3.534A pdb=" N GLU A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 247 removed outlier: 4.143A pdb=" N THR A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.525A pdb=" N ALA A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 removed outlier: 3.703A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.550A pdb=" N ALA A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 309 removed outlier: 3.595A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 351 removed outlier: 3.704A pdb=" N PHE A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Proline residue: A 340 - end of helix removed outlier: 3.551A pdb=" N PHE A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.716A pdb=" N CYS A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.608A pdb=" N THR A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.642A pdb=" N LEU A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 356 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 102 through 106 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.524A pdb=" N GLN C 5 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 59 removed outlier: 3.647A pdb=" N ASN C 58 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG C 38 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET C 34 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR C 37 " --> pdb=" O TYR C 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 72 252 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.52 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 572 1.31 - 1.44: 989 1.44 - 1.56: 2006 1.56 - 1.69: 0 1.69 - 1.82: 29 Bond restraints: 3596 Sorted by residual: bond pdb=" C10 IXO A 500 " pdb=" N11 IXO A 500 " ideal model delta sigma weight residual 1.270 1.450 -0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" C05 IXO A 500 " pdb=" C06 IXO A 500 " ideal model delta sigma weight residual 1.450 1.528 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C10 IXO A 500 " pdb=" O09 IXO A 500 " ideal model delta sigma weight residual 1.325 1.399 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C07 IXO A 500 " pdb=" C08 IXO A 500 " ideal model delta sigma weight residual 1.454 1.527 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C05 IXO A 500 " pdb=" N02 IXO A 500 " ideal model delta sigma weight residual 1.504 1.451 0.053 2.00e-02 2.50e+03 6.95e+00 ... (remaining 3591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 4775 1.63 - 3.26: 123 3.26 - 4.89: 24 4.89 - 6.52: 8 6.52 - 8.15: 4 Bond angle restraints: 4934 Sorted by residual: angle pdb=" N TYR C 33 " pdb=" CA TYR C 33 " pdb=" C TYR C 33 " ideal model delta sigma weight residual 107.61 115.45 -7.84 1.74e+00 3.30e-01 2.03e+01 angle pdb=" N HIS A 90 " pdb=" CA HIS A 90 " pdb=" CB HIS A 90 " ideal model delta sigma weight residual 111.39 103.79 7.60 1.75e+00 3.27e-01 1.89e+01 angle pdb=" C GLN C 105 " pdb=" CA GLN C 105 " pdb=" CB GLN C 105 " ideal model delta sigma weight residual 111.95 106.27 5.68 1.50e+00 4.44e-01 1.43e+01 angle pdb=" N ARG C 106 " pdb=" CA ARG C 106 " pdb=" C ARG C 106 " ideal model delta sigma weight residual 113.16 117.83 -4.67 1.24e+00 6.50e-01 1.42e+01 angle pdb=" CA GLN C 105 " pdb=" C GLN C 105 " pdb=" O GLN C 105 " ideal model delta sigma weight residual 122.03 118.13 3.90 1.17e+00 7.31e-01 1.11e+01 ... (remaining 4929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.66: 1881 13.66 - 27.32: 138 27.32 - 40.97: 62 40.97 - 54.63: 10 54.63 - 68.29: 4 Dihedral angle restraints: 2095 sinusoidal: 593 harmonic: 1502 Sorted by residual: dihedral pdb=" CB CYS A 351 " pdb=" SG CYS A 351 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -124.42 38.42 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" N HIS A 90 " pdb=" C HIS A 90 " pdb=" CA HIS A 90 " pdb=" CB HIS A 90 " ideal model delta harmonic sigma weight residual 122.80 113.06 9.74 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" CA THR C 50 " pdb=" C THR C 50 " pdb=" N ILE C 51 " pdb=" CA ILE C 51 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 2092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 507 0.056 - 0.111: 82 0.111 - 0.167: 7 0.167 - 0.222: 1 0.222 - 0.278: 3 Chirality restraints: 600 Sorted by residual: chirality pdb=" CA HIS A 90 " pdb=" N HIS A 90 " pdb=" C HIS A 90 " pdb=" CB HIS A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA VAL C 104 " pdb=" N VAL C 104 " pdb=" C VAL C 104 " pdb=" CB VAL C 104 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA GLN C 105 " pdb=" N GLN C 105 " pdb=" C GLN C 105 " pdb=" CB GLN C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 597 not shown) Planarity restraints: 625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 89 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.88e+00 pdb=" C GLY A 89 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY A 89 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS A 90 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 158 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 159 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 199 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 200 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.019 5.00e-02 4.00e+02 ... (remaining 622 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 1642 2.97 - 3.45: 3760 3.45 - 3.93: 5652 3.93 - 4.42: 6665 4.42 - 4.90: 10610 Nonbonded interactions: 28329 Sorted by model distance: nonbonded pdb=" O MET A 344 " pdb=" OG SER A 348 " model vdw 2.484 3.040 nonbonded pdb=" O VAL C 104 " pdb=" C GLN C 105 " model vdw 2.487 3.270 nonbonded pdb=" O LYS A 352 " pdb=" O ARG C 106 " model vdw 2.533 3.040 nonbonded pdb=" O ASN B 357 " pdb=" OD1 ASN B 357 " model vdw 2.541 3.040 nonbonded pdb=" CB SER A 348 " pdb=" NH1 ARG C 106 " model vdw 2.565 3.520 ... (remaining 28324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.610 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 3599 Z= 0.254 Angle : 0.695 8.145 4940 Z= 0.404 Chirality : 0.046 0.278 600 Planarity : 0.004 0.035 625 Dihedral : 12.703 68.288 1114 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.42 % Allowed : 1.07 % Favored : 97.51 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.35), residues: 501 helix: -0.43 (0.27), residues: 321 sheet: -3.39 (0.80), residues: 39 loop : -2.43 (0.46), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 99 TYR 0.017 0.001 TYR C 37 PHE 0.013 0.001 PHE A 197 TRP 0.009 0.001 TRP A 338 HIS 0.008 0.003 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.25 ( 3596) covalent geometry : angle 0.69555 / 0.40 ( 4934) SS BOND : bond 0.00144 / 0.07 ( 3) SS BOND : angle 0.58827 / 0.36 ( 6) hydrogen bonds : bond 0.20161 / 13.77 ( 252) hydrogen bonds : angle 8.69403 / 6.49 ( 735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.131 Fit side-chains REVERT: A 285 GLU cc_start: 0.7183 (pt0) cc_final: 0.6923 (pt0) REVERT: A 322 LYS cc_start: 0.7313 (tttt) cc_final: 0.6898 (ttmm) REVERT: C 79 TYR cc_start: 0.6543 (m-80) cc_final: 0.5629 (t80) outliers start: 4 outliers final: 0 residues processed: 72 average time/residue: 0.4666 time to fit residues: 34.7238 Evaluate side-chains 54 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.0170 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN C 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.216085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.194975 restraints weight = 4232.281| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 1.54 r_work: 0.4095 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3599 Z= 0.145 Angle : 0.586 6.202 4940 Z= 0.317 Chirality : 0.043 0.158 600 Planarity : 0.005 0.042 625 Dihedral : 4.712 23.129 555 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.78 % Allowed : 11.03 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.37), residues: 501 helix: 0.85 (0.28), residues: 327 sheet: -2.87 (0.93), residues: 28 loop : -2.65 (0.44), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 171 TYR 0.025 0.001 TYR C 33 PHE 0.018 0.001 PHE A 197 TRP 0.010 0.001 TRP A 360 HIS 0.006 0.003 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 ( 3596) covalent geometry : angle 0.58637 / 0.32 ( 4934) SS BOND : bond 0.00368 / 0.18 ( 3) SS BOND : angle 0.66275 / 0.35 ( 6) hydrogen bonds : bond 0.03965 / 2.85 ( 252) hydrogen bonds : angle 4.94227 / 3.64 ( 735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.122 Fit side-chains REVERT: A 170 GLU cc_start: 0.6716 (tt0) cc_final: 0.5710 (mt-10) REVERT: A 228 LYS cc_start: 0.7649 (ttmm) cc_final: 0.7399 (ttmm) REVERT: A 262 ASN cc_start: 0.6642 (m-40) cc_final: 0.6054 (t0) REVERT: A 285 GLU cc_start: 0.6852 (pt0) cc_final: 0.6479 (tp30) REVERT: B 350 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8432 (mm-40) REVERT: C 79 TYR cc_start: 0.6570 (m-80) cc_final: 0.5790 (t80) REVERT: C 101 TYR cc_start: 0.6942 (p90) cc_final: 0.6584 (p90) outliers start: 5 outliers final: 2 residues processed: 57 average time/residue: 0.4219 time to fit residues: 25.0141 Evaluate side-chains 47 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 373 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.215037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.194032 restraints weight = 4208.613| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.53 r_work: 0.4125 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3599 Z= 0.165 Angle : 0.594 7.114 4940 Z= 0.315 Chirality : 0.044 0.311 600 Planarity : 0.004 0.031 625 Dihedral : 4.734 22.546 555 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.20 % Allowed : 12.46 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.37), residues: 501 helix: 1.02 (0.28), residues: 331 sheet: -2.38 (1.12), residues: 21 loop : -2.92 (0.42), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 171 TYR 0.017 0.001 TYR C 101 PHE 0.016 0.002 PHE A 197 TRP 0.009 0.001 TRP A 360 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 ( 3596) covalent geometry : angle 0.59454 / 0.31 ( 4934) SS BOND : bond 0.00247 / 0.12 ( 3) SS BOND : angle 0.44478 / 0.27 ( 6) hydrogen bonds : bond 0.04040 / 2.90 ( 252) hydrogen bonds : angle 4.79721 / 3.51 ( 735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.126 Fit side-chains REVERT: A 170 GLU cc_start: 0.6673 (tt0) cc_final: 0.5682 (mt-10) REVERT: A 183 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5661 (tt) REVERT: A 262 ASN cc_start: 0.6666 (m-40) cc_final: 0.6123 (t0) REVERT: A 285 GLU cc_start: 0.6886 (pt0) cc_final: 0.6539 (tp30) REVERT: B 350 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8491 (mm-40) REVERT: C 34 MET cc_start: 0.7496 (ttm) cc_final: 0.7200 (mtp) REVERT: C 79 TYR cc_start: 0.6715 (m-80) cc_final: 0.5889 (t80) outliers start: 9 outliers final: 4 residues processed: 50 average time/residue: 0.3912 time to fit residues: 20.3260 Evaluate side-chains 49 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 33 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.0870 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN C 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.215036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.194099 restraints weight = 4192.419| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 1.53 r_work: 0.4089 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3998 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3599 Z= 0.167 Angle : 0.595 7.114 4940 Z= 0.315 Chirality : 0.044 0.311 600 Planarity : 0.004 0.031 625 Dihedral : 4.738 22.546 555 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.14 % Allowed : 13.52 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.37), residues: 501 helix: 1.02 (0.28), residues: 331 sheet: -2.38 (1.12), residues: 21 loop : -2.92 (0.42), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 171 TYR 0.017 0.001 TYR C 101 PHE 0.016 0.002 PHE A 197 TRP 0.009 0.001 TRP A 360 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 3596) covalent geometry : angle 0.59533 / 0.32 ( 4934) SS BOND : bond 0.00247 / 0.12 ( 3) SS BOND : angle 0.44477 / 0.27 ( 6) hydrogen bonds : bond 0.04040 / 2.90 ( 252) hydrogen bonds : angle 4.79721 / 3.51 ( 735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.093 Fit side-chains REVERT: A 170 GLU cc_start: 0.6685 (tt0) cc_final: 0.5696 (mt-10) REVERT: A 183 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5679 (tt) REVERT: A 262 ASN cc_start: 0.6693 (m-40) cc_final: 0.6124 (t0) REVERT: A 285 GLU cc_start: 0.6902 (pt0) cc_final: 0.6537 (tp30) REVERT: B 350 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8488 (mm-40) REVERT: C 34 MET cc_start: 0.7488 (ttm) cc_final: 0.7192 (mtp) REVERT: C 79 TYR cc_start: 0.6733 (m-80) cc_final: 0.5883 (t80) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.3861 time to fit residues: 18.4413 Evaluate side-chains 49 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 33 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.215036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.194122 restraints weight = 4178.221| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.53 r_work: 0.4089 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3997 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3599 Z= 0.167 Angle : 0.595 7.114 4940 Z= 0.315 Chirality : 0.044 0.311 600 Planarity : 0.004 0.031 625 Dihedral : 4.734 22.546 555 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.14 % Allowed : 13.52 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.37), residues: 501 helix: 1.02 (0.28), residues: 331 sheet: -2.38 (1.12), residues: 21 loop : -2.92 (0.42), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 171 TYR 0.017 0.001 TYR C 101 PHE 0.016 0.002 PHE A 197 TRP 0.009 0.001 TRP A 360 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 3596) covalent geometry : angle 0.59533 / 0.32 ( 4934) SS BOND : bond 0.00247 / 0.12 ( 3) SS BOND : angle 0.44477 / 0.27 ( 6) hydrogen bonds : bond 0.04040 / 2.90 ( 252) hydrogen bonds : angle 4.79721 / 3.51 ( 735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.134 Fit side-chains REVERT: A 170 GLU cc_start: 0.6684 (tt0) cc_final: 0.5694 (mt-10) REVERT: A 183 LEU cc_start: 0.5933 (OUTLIER) cc_final: 0.5681 (tt) REVERT: A 262 ASN cc_start: 0.6690 (m-40) cc_final: 0.6116 (t0) REVERT: A 285 GLU cc_start: 0.6912 (pt0) cc_final: 0.6534 (tp30) REVERT: B 350 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8489 (mm-40) REVERT: C 34 MET cc_start: 0.7490 (ttm) cc_final: 0.7192 (mtp) REVERT: C 79 TYR cc_start: 0.6734 (m-80) cc_final: 0.5876 (t80) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.4445 time to fit residues: 21.2306 Evaluate side-chains 49 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 33 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 10 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.4372 > 50:) chunk 15 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.216057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.195305 restraints weight = 4209.043| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 1.53 r_work: 0.4129 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3599 Z= 0.135 Angle : 0.567 6.852 4940 Z= 0.301 Chirality : 0.043 0.210 600 Planarity : 0.004 0.030 625 Dihedral : 4.566 21.631 555 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.99 % Favored : 95.81 % Rotamer: Outliers : 2.85 % Allowed : 12.46 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.37), residues: 501 helix: 1.19 (0.29), residues: 332 sheet: -2.71 (1.03), residues: 23 loop : -2.74 (0.43), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 171 TYR 0.010 0.001 TYR C 101 PHE 0.015 0.001 PHE A 197 TRP 0.009 0.001 TRP A 360 HIS 0.003 0.002 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 3596) covalent geometry : angle 0.56723 / 0.30 ( 4934) SS BOND : bond 0.00293 / 0.14 ( 3) SS BOND : angle 0.47827 / 0.32 ( 6) hydrogen bonds : bond 0.03903 / 2.82 ( 252) hydrogen bonds : angle 4.51360 / 3.30 ( 735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.133 Fit side-chains REVERT: A 170 GLU cc_start: 0.6658 (tt0) cc_final: 0.5659 (mt-10) REVERT: A 262 ASN cc_start: 0.6746 (m-40) cc_final: 0.6127 (t0) REVERT: A 285 GLU cc_start: 0.6842 (pt0) cc_final: 0.6486 (tp30) REVERT: B 350 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8483 (mm-40) REVERT: C 34 MET cc_start: 0.7444 (ttm) cc_final: 0.7118 (mtp) REVERT: C 79 TYR cc_start: 0.6839 (m-80) cc_final: 0.6005 (t80) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.4179 time to fit residues: 22.5898 Evaluate side-chains 48 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain C residue 33 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN C 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.215545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.194687 restraints weight = 4240.666| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 1.54 r_work: 0.4114 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4020 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3599 Z= 0.154 Angle : 0.574 6.838 4940 Z= 0.305 Chirality : 0.043 0.240 600 Planarity : 0.004 0.063 625 Dihedral : 4.632 21.483 555 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.19 % Favored : 95.61 % Rotamer: Outliers : 3.56 % Allowed : 12.46 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.37), residues: 501 helix: 1.23 (0.28), residues: 332 sheet: -2.31 (1.12), residues: 21 loop : -2.76 (0.43), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 106 TYR 0.014 0.001 TYR C 101 PHE 0.014 0.001 PHE A 197 TRP 0.009 0.001 TRP A 360 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 3596) covalent geometry : angle 0.57435 / 0.31 ( 4934) SS BOND : bond 0.00263 / 0.13 ( 3) SS BOND : angle 0.41469 / 0.27 ( 6) hydrogen bonds : bond 0.03930 / 2.83 ( 252) hydrogen bonds : angle 4.52153 / 3.30 ( 735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.079 Fit side-chains REVERT: A 170 GLU cc_start: 0.6590 (tt0) cc_final: 0.5639 (mt-10) REVERT: A 262 ASN cc_start: 0.6720 (m-40) cc_final: 0.6105 (t0) REVERT: A 285 GLU cc_start: 0.6865 (pt0) cc_final: 0.6490 (tp30) REVERT: B 350 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8418 (mm-40) REVERT: C 34 MET cc_start: 0.7426 (ttm) cc_final: 0.7097 (mtp) REVERT: C 79 TYR cc_start: 0.6859 (m-80) cc_final: 0.6033 (t80) outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 0.3032 time to fit residues: 15.7769 Evaluate side-chains 51 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain C residue 33 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 22 optimal weight: 0.0020 chunk 44 optimal weight: 4.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.215530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.194448 restraints weight = 4274.862| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 1.57 r_work: 0.4129 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3599 Z= 0.155 Angle : 0.575 6.837 4940 Z= 0.305 Chirality : 0.043 0.240 600 Planarity : 0.004 0.063 625 Dihedral : 4.631 21.483 555 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.19 % Favored : 95.61 % Rotamer: Outliers : 2.49 % Allowed : 13.52 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.37), residues: 501 helix: 1.23 (0.28), residues: 332 sheet: -2.31 (1.12), residues: 21 loop : -2.76 (0.43), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 106 TYR 0.014 0.001 TYR C 101 PHE 0.014 0.001 PHE A 197 TRP 0.009 0.001 TRP A 360 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 3596) covalent geometry : angle 0.57484 / 0.31 ( 4934) SS BOND : bond 0.00263 / 0.13 ( 3) SS BOND : angle 0.41469 / 0.27 ( 6) hydrogen bonds : bond 0.03930 / 2.83 ( 252) hydrogen bonds : angle 4.52153 / 3.30 ( 735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.126 Fit side-chains REVERT: A 170 GLU cc_start: 0.6586 (tt0) cc_final: 0.5621 (mt-10) REVERT: A 262 ASN cc_start: 0.6702 (m-40) cc_final: 0.6099 (t0) REVERT: A 285 GLU cc_start: 0.6869 (pt0) cc_final: 0.6488 (tp30) REVERT: B 350 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8421 (mm-40) REVERT: C 34 MET cc_start: 0.7431 (ttm) cc_final: 0.7101 (mtp) REVERT: C 79 TYR cc_start: 0.6860 (m-80) cc_final: 0.6027 (t80) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.3174 time to fit residues: 15.8737 Evaluate side-chains 51 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain C residue 33 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.0470 chunk 21 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.215493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.194600 restraints weight = 4163.633| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 1.53 r_work: 0.4133 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3599 Z= 0.154 Angle : 0.574 6.802 4940 Z= 0.305 Chirality : 0.043 0.242 600 Planarity : 0.004 0.063 625 Dihedral : 4.648 24.615 555 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.19 % Favored : 95.61 % Rotamer: Outliers : 2.49 % Allowed : 13.52 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.37), residues: 501 helix: 1.23 (0.28), residues: 332 sheet: -2.31 (1.12), residues: 21 loop : -2.76 (0.43), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 106 TYR 0.015 0.001 TYR C 101 PHE 0.013 0.001 PHE A 197 TRP 0.009 0.001 TRP A 360 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 3596) covalent geometry : angle 0.57439 / 0.31 ( 4934) SS BOND : bond 0.00262 / 0.13 ( 3) SS BOND : angle 0.41468 / 0.27 ( 6) hydrogen bonds : bond 0.03930 / 2.83 ( 252) hydrogen bonds : angle 4.52188 / 3.30 ( 735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.074 Fit side-chains REVERT: A 170 GLU cc_start: 0.6584 (tt0) cc_final: 0.5631 (mt-10) REVERT: A 262 ASN cc_start: 0.6706 (m-40) cc_final: 0.6112 (t0) REVERT: A 285 GLU cc_start: 0.6856 (pt0) cc_final: 0.6490 (tp30) REVERT: B 350 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8419 (mm-40) REVERT: C 34 MET cc_start: 0.7427 (ttm) cc_final: 0.7097 (mtp) REVERT: C 79 TYR cc_start: 0.6854 (m-80) cc_final: 0.6031 (t80) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.4195 time to fit residues: 20.8230 Evaluate side-chains 51 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain C residue 33 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 0.0470 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 0.0870 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.215699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.194808 restraints weight = 4238.988| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 1.55 r_work: 0.4134 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4039 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3599 Z= 0.140 Angle : 0.599 10.422 4940 Z= 0.311 Chirality : 0.044 0.293 600 Planarity : 0.005 0.094 625 Dihedral : 4.621 21.551 555 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.79 % Favored : 96.01 % Rotamer: Outliers : 2.85 % Allowed : 13.17 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.38), residues: 501 helix: 1.28 (0.28), residues: 332 sheet: -2.18 (1.15), residues: 21 loop : -2.70 (0.43), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 106 TYR 0.012 0.001 TYR C 101 PHE 0.015 0.001 PHE A 197 TRP 0.009 0.001 TRP A 360 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 3596) covalent geometry : angle 0.59892 / 0.31 ( 4934) SS BOND : bond 0.00270 / 0.13 ( 3) SS BOND : angle 0.41849 / 0.29 ( 6) hydrogen bonds : bond 0.03865 / 2.79 ( 252) hydrogen bonds : angle 4.51069 / 3.27 ( 735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1002 Ramachandran restraints generated. 501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.076 Fit side-chains REVERT: A 170 GLU cc_start: 0.6651 (tt0) cc_final: 0.5657 (mt-10) REVERT: B 350 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8498 (mm-40) REVERT: C 34 MET cc_start: 0.7266 (ttm) cc_final: 0.6939 (mtp) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.3024 time to fit residues: 15.4206 Evaluate side-chains 51 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain C residue 33 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.0070 chunk 10 optimal weight: 0.0000 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.216256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.195318 restraints weight = 4196.823| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 1.55 r_work: 0.4124 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4028 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3599 Z= 0.129 Angle : 0.605 9.669 4940 Z= 0.313 Chirality : 0.044 0.311 600 Planarity : 0.005 0.081 625 Dihedral : 4.586 21.385 555 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.19 % Favored : 95.61 % Rotamer: Outliers : 2.49 % Allowed : 13.88 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.38), residues: 501 helix: 1.31 (0.29), residues: 332 sheet: -2.47 (1.08), residues: 23 loop : -2.65 (0.44), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 106 TYR 0.013 0.001 TYR A 208 PHE 0.014 0.001 PHE A 197 TRP 0.008 0.001 TRP A 360 HIS 0.003 0.002 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 3596) covalent geometry : angle 0.60525 / 0.31 ( 4934) SS BOND : bond 0.00250 / 0.12 ( 3) SS BOND : angle 0.37196 / 0.27 ( 6) hydrogen bonds : bond 0.03895 / 2.81 ( 252) hydrogen bonds : angle 4.50694 / 3.26 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1167.81 seconds wall clock time: 20 minutes 34.53 seconds (1234.53 seconds total)