Starting phenix.real_space_refine on Tue Aug 4 17:14:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25pv_80292/08_2026/25pv_80292.cif Found real_map, /net/cci-nas-00/data/ceres_data/25pv_80292/08_2026/25pv_80292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/25pv_80292/08_2026/25pv_80292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25pv_80292/08_2026/25pv_80292.map" model { file = "/net/cci-nas-00/data/ceres_data/25pv_80292/08_2026/25pv_80292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25pv_80292/08_2026/25pv_80292.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.092 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 12 5.16 5 C 3280 2.51 5 N 875 2.21 5 O 1030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 5197 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1927 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 232} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1635 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 1.35, per 1000 atoms: 0.26 Number of scatterers: 5197 At special positions: 0 Unit cell: (66, 67.5, 132.75, 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 12 16.00 O 1030 8.00 N 875 7.00 C 3280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 132.7 milliseconds 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 11 sheets defined 15.9% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 40 through 48 removed outlier: 3.927A pdb=" N LYS A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 309 through 312 Processing helix chain 'A' and resid 313 through 321 removed outlier: 3.669A pdb=" N ILE A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.656A pdb=" N PHE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 388 through 403 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.120A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 183 through 189 removed outlier: 3.756A pdb=" N HIS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 334 through 338 removed outlier: 3.963A pdb=" N VAL A 334 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 326 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 323 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE A 424 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 325 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ASP A 426 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 7 removed outlier: 5.808A pdb=" N GLN C 16 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER C 86 " --> pdb=" O GLN C 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER C 72 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.564A pdb=" N ALA C 93 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TRP C 36 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR C 52 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TRP C 38 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 46 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.564A pdb=" N ALA C 93 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 124 through 128 removed outlier: 3.627A pdb=" N PHE C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR C 180 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 124 through 128 removed outlier: 3.627A pdb=" N PHE C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR C 180 " --> pdb=" O ASP C 148 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 173 " --> pdb=" O SER C 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 155 through 158 removed outlier: 4.476A pdb=" N TYR C 198 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.010A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.676A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 145 through 150 removed outlier: 3.721A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS D 194 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) 187 hydrogen bonds defined for protein. 483 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: 0.65 Time building geometry restraints manager: 0.36 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: 1686 1.34 - 1.46: 1206 1.46 - 1.58: 2404 1.58 - 1.70: 0 1.70 - 1.82: 14 Bond restraints: 5310 Sorted by residual: bond pdb=" CB PRO A 6 " pdb=" CG PRO A 6 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.75e+00 bond pdb=" CB PRO D 15 " pdb=" CG PRO D 15 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.38e+00 bond pdb=" N GLY A 365 " pdb=" CA GLY A 365 " ideal model delta sigma weight residual 1.449 1.465 -0.016 1.45e-02 4.76e+03 1.25e+00 bond pdb=" CB GLU A 319 " pdb=" CG GLU A 319 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CA VAL A 29 " pdb=" CB VAL A 29 " ideal model delta sigma weight residual 1.540 1.553 -0.013 1.36e-02 5.41e+03 8.69e-01 ... (remaining 5305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 7094 1.81 - 3.62: 118 3.62 - 5.43: 17 5.43 - 7.25: 3 7.25 - 9.06: 3 Bond angle restraints: 7235 Sorted by residual: angle pdb=" N GLY A 365 " pdb=" CA GLY A 365 " pdb=" C GLY A 365 " ideal model delta sigma weight residual 113.18 122.24 -9.06 2.37e+00 1.78e-01 1.46e+01 angle pdb=" CA PRO A 6 " pdb=" N PRO A 6 " pdb=" CD PRO A 6 " ideal model delta sigma weight residual 112.00 106.87 5.13 1.40e+00 5.10e-01 1.34e+01 angle pdb=" CA PRO D 15 " pdb=" N PRO D 15 " pdb=" CD PRO D 15 " ideal model delta sigma weight residual 112.00 107.30 4.70 1.40e+00 5.10e-01 1.13e+01 angle pdb=" C ASN D 93 " pdb=" N TRP D 94 " pdb=" CA TRP D 94 " ideal model delta sigma weight residual 121.80 113.99 7.81 2.44e+00 1.68e-01 1.03e+01 angle pdb=" CA VAL A 29 " pdb=" CB VAL A 29 " pdb=" CG1 VAL A 29 " ideal model delta sigma weight residual 110.40 115.20 -4.80 1.70e+00 3.46e-01 7.99e+00 ... (remaining 7230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2783 17.97 - 35.95: 322 35.95 - 53.92: 70 53.92 - 71.89: 17 71.89 - 89.87: 4 Dihedral angle restraints: 3196 sinusoidal: 1212 harmonic: 1984 Sorted by residual: dihedral pdb=" CA TRP D 94 " pdb=" C TRP D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta harmonic sigma weight residual 180.00 130.08 49.92 0 5.00e+00 4.00e-02 9.97e+01 dihedral pdb=" CB CYS C 144 " pdb=" SG CYS C 144 " pdb=" SG CYS C 200 " pdb=" CB CYS C 200 " ideal model delta sinusoidal sigma weight residual 93.00 143.42 -50.42 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 97 " pdb=" CB CYS C 97 " ideal model delta sinusoidal sigma weight residual 93.00 45.15 47.85 1 1.00e+01 1.00e-02 3.16e+01 ... (remaining 3193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 489 0.029 - 0.057: 192 0.057 - 0.086: 79 0.086 - 0.115: 54 0.115 - 0.143: 14 Chirality restraints: 828 Sorted by residual: chirality pdb=" CA ILE D 75 " pdb=" N ILE D 75 " pdb=" C ILE D 75 " pdb=" CB ILE D 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE D 48 " pdb=" N ILE D 48 " pdb=" C ILE D 48 " pdb=" CB ILE D 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE D 58 " pdb=" N ILE D 58 " pdb=" C ILE D 58 " pdb=" CB ILE D 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 825 not shown) Planarity restraints: 934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 5 " 0.084 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO A 6 " -0.216 5.00e-02 4.00e+02 pdb=" CA PRO A 6 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO A 6 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 14 " 0.049 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO D 15 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 15 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 15 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 94 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO D 95 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.034 5.00e-02 4.00e+02 ... (remaining 931 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 749 2.76 - 3.29: 4739 3.29 - 3.83: 8274 3.83 - 4.36: 9613 4.36 - 4.90: 17327 Nonbonded interactions: 40702 Sorted by model distance: nonbonded pdb=" O PHE A 383 " pdb=" OH TYR A 408 " model vdw 2.224 3.040 nonbonded pdb=" O ASP A 388 " pdb=" OG SER A 392 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR C 17 " pdb=" O LEU C 84 " model vdw 2.302 3.040 nonbonded pdb=" OD1 ASP D 151 " pdb=" ND1 HIS D 189 " model vdw 2.315 3.120 nonbonded pdb=" NZ LYS D 39 " pdb=" O GLU D 81 " model vdw 2.320 3.120 ... (remaining 40697 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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 0.083 5314 Z= 0.132 Angle : 0.611 9.058 7243 Z= 0.319 Chirality : 0.043 0.143 828 Planarity : 0.007 0.125 934 Dihedral : 16.174 89.865 1908 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.52 % Allowed : 27.13 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.72 (0.32), residues: 671 helix: 0.25 (0.62), residues: 74 sheet: -0.14 (0.36), residues: 209 loop : -0.79 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 103 TYR 0.012 0.001 TYR C 35 PHE 0.013 0.001 PHE C 80 TRP 0.006 0.001 TRP C 158 HIS 0.002 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 5310) covalent geometry : angle 0.60905 / 0.32 ( 7235) SS BOND : bond 0.00331 / 0.16 ( 4) SS BOND : angle 1.50862 / 0.82 ( 8) hydrogen bonds : bond 0.25842 / 18.25 ( 169) hydrogen bonds : angle 9.69023 / 7.09 ( 483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.124 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 44 average time/residue: 0.0728 time to fit residues: 4.2313 Evaluate side-chains 43 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 91 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.193266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.157342 restraints weight = 6576.019| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.50 r_work: 0.3774 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5314 Z= 0.111 Angle : 0.577 7.814 7243 Z= 0.299 Chirality : 0.043 0.160 828 Planarity : 0.006 0.082 934 Dihedral : 5.687 49.434 736 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.83 % Allowed : 23.65 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.59 (0.33), residues: 671 helix: 0.33 (0.61), residues: 80 sheet: 0.23 (0.35), residues: 217 loop : -0.92 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 103 TYR 0.011 0.001 TYR C 49 PHE 0.014 0.001 PHE C 80 TRP 0.007 0.001 TRP C 158 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 5310) covalent geometry : angle 0.57438 / 0.30 ( 7235) SS BOND : bond 0.00364 / 0.18 ( 4) SS BOND : angle 1.68598 / 0.89 ( 8) hydrogen bonds : bond 0.03820 / 2.65 ( 169) hydrogen bonds : angle 6.76514 / 4.95 ( 483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.156 Fit side-chains REVERT: A 21 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7349 (tt0) outliers start: 22 outliers final: 10 residues processed: 57 average time/residue: 0.0738 time to fit residues: 5.4438 Evaluate side-chains 46 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.191861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.155690 restraints weight = 6535.756| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.49 r_work: 0.3748 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5314 Z= 0.128 Angle : 0.586 7.809 7243 Z= 0.300 Chirality : 0.044 0.149 828 Planarity : 0.005 0.069 934 Dihedral : 5.925 50.280 736 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.17 % Allowed : 24.87 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.64 (0.32), residues: 671 helix: 0.31 (0.61), residues: 80 sheet: 0.22 (0.35), residues: 217 loop : -0.98 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.015 0.001 TYR C 96 PHE 0.015 0.001 PHE C 80 TRP 0.007 0.001 TRP C 158 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 5310) covalent geometry : angle 0.58327 / 0.30 ( 7235) SS BOND : bond 0.00413 / 0.21 ( 4) SS BOND : angle 1.84794 / 1.04 ( 8) hydrogen bonds : bond 0.03545 / 2.44 ( 169) hydrogen bonds : angle 6.22730 / 4.53 ( 483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 36 time to evaluate : 0.115 Fit side-chains REVERT: A 21 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: A 28 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: D 75 ILE cc_start: 0.7181 (mm) cc_final: 0.6889 (mm) outliers start: 24 outliers final: 11 residues processed: 54 average time/residue: 0.0818 time to fit residues: 5.5876 Evaluate side-chains 46 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 52 optimal weight: 0.0050 chunk 22 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.191466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.155621 restraints weight = 6551.345| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.47 r_work: 0.3743 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5314 Z= 0.133 Angle : 0.583 7.939 7243 Z= 0.299 Chirality : 0.044 0.147 828 Planarity : 0.005 0.065 934 Dihedral : 6.314 53.527 736 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.62 % Favored : 95.23 % Rotamer: Outliers : 4.70 % Allowed : 24.70 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.64 (0.32), residues: 671 helix: 0.30 (0.61), residues: 80 sheet: 0.26 (0.35), residues: 217 loop : -1.00 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.015 0.001 TYR C 96 PHE 0.016 0.001 PHE C 80 TRP 0.007 0.001 TRP C 158 HIS 0.003 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 5310) covalent geometry : angle 0.57943 / 0.30 ( 7235) SS BOND : bond 0.00515 / 0.26 ( 4) SS BOND : angle 1.90864 / 1.09 ( 8) hydrogen bonds : bond 0.03285 / 2.25 ( 169) hydrogen bonds : angle 5.99836 / 4.35 ( 483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 40 time to evaluate : 0.121 Fit side-chains REVERT: A 21 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: A 28 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6992 (m-30) REVERT: D 103 LYS cc_start: 0.7775 (tttp) cc_final: 0.7409 (tttm) outliers start: 27 outliers final: 15 residues processed: 60 average time/residue: 0.0775 time to fit residues: 5.8249 Evaluate side-chains 52 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 191 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.191841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.155934 restraints weight = 6689.766| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.48 r_work: 0.3750 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5314 Z= 0.121 Angle : 0.567 7.951 7243 Z= 0.290 Chirality : 0.044 0.147 828 Planarity : 0.005 0.062 934 Dihedral : 6.334 55.242 736 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.32 % Favored : 95.38 % Rotamer: Outliers : 4.00 % Allowed : 25.91 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.66 (0.32), residues: 671 helix: 0.27 (0.62), residues: 79 sheet: 0.28 (0.35), residues: 217 loop : -1.03 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.015 0.001 TYR C 96 PHE 0.015 0.001 PHE C 80 TRP 0.006 0.001 TRP A 59 HIS 0.003 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 5310) covalent geometry : angle 0.56409 / 0.29 ( 7235) SS BOND : bond 0.00594 / 0.29 ( 4) SS BOND : angle 1.88574 / 1.05 ( 8) hydrogen bonds : bond 0.03060 / 2.10 ( 169) hydrogen bonds : angle 5.82674 / 4.21 ( 483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 38 time to evaluate : 0.157 Fit side-chains REVERT: A 21 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: A 28 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6974 (m-30) REVERT: D 103 LYS cc_start: 0.7731 (tttp) cc_final: 0.7451 (tttm) outliers start: 23 outliers final: 16 residues processed: 55 average time/residue: 0.0825 time to fit residues: 5.7542 Evaluate side-chains 54 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 23 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.192653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156482 restraints weight = 6649.371| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.52 r_work: 0.3759 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5314 Z= 0.110 Angle : 0.556 7.898 7243 Z= 0.283 Chirality : 0.044 0.153 828 Planarity : 0.005 0.060 934 Dihedral : 5.734 51.600 736 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.73 % Favored : 95.98 % Rotamer: Outliers : 4.35 % Allowed : 26.09 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.61 (0.33), residues: 671 helix: 0.32 (0.62), residues: 79 sheet: 0.33 (0.35), residues: 217 loop : -1.02 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 91 TYR 0.014 0.001 TYR C 96 PHE 0.015 0.001 PHE C 80 TRP 0.006 0.001 TRP A 59 HIS 0.003 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 5310) covalent geometry : angle 0.55292 / 0.28 ( 7235) SS BOND : bond 0.00384 / 0.19 ( 4) SS BOND : angle 1.76644 / 0.99 ( 8) hydrogen bonds : bond 0.02883 / 1.97 ( 169) hydrogen bonds : angle 5.65981 / 4.08 ( 483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 37 time to evaluate : 0.118 Fit side-chains REVERT: A 21 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: A 28 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6969 (m-30) REVERT: A 64 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: A 291 ASN cc_start: 0.5899 (OUTLIER) cc_final: 0.5462 (p0) REVERT: D 103 LYS cc_start: 0.7677 (tttp) cc_final: 0.7427 (tttm) outliers start: 25 outliers final: 16 residues processed: 56 average time/residue: 0.0676 time to fit residues: 4.8945 Evaluate side-chains 56 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 191 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.195947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.160002 restraints weight = 6598.021| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.51 r_work: 0.3796 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5314 Z= 0.085 Angle : 0.517 7.672 7243 Z= 0.263 Chirality : 0.042 0.149 828 Planarity : 0.005 0.058 934 Dihedral : 5.230 51.832 732 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.43 % Favored : 96.27 % Rotamer: Outliers : 3.65 % Allowed : 26.43 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.44 (0.33), residues: 671 helix: 0.71 (0.63), residues: 79 sheet: 0.44 (0.35), residues: 217 loop : -0.97 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.010 0.001 TYR C 96 PHE 0.014 0.001 PHE C 80 TRP 0.005 0.001 TRP A 59 HIS 0.003 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.08 ( 5310) covalent geometry : angle 0.51518 / 0.26 ( 7235) SS BOND : bond 0.00285 / 0.14 ( 4) SS BOND : angle 1.39422 / 0.78 ( 8) hydrogen bonds : bond 0.02502 / 1.70 ( 169) hydrogen bonds : angle 5.31854 / 3.80 ( 483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.192 Fit side-chains REVERT: A 28 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6824 (m-30) REVERT: A 291 ASN cc_start: 0.5788 (OUTLIER) cc_final: 0.5322 (p0) outliers start: 21 outliers final: 15 residues processed: 56 average time/residue: 0.0626 time to fit residues: 4.8100 Evaluate side-chains 50 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 191 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 0.0570 chunk 48 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.193505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.157847 restraints weight = 6597.895| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.47 r_work: 0.3769 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5314 Z= 0.107 Angle : 0.545 7.870 7243 Z= 0.278 Chirality : 0.043 0.158 828 Planarity : 0.005 0.059 934 Dihedral : 5.365 52.329 732 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.13 % Favored : 96.57 % Rotamer: Outliers : 4.00 % Allowed : 25.91 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.44 (0.33), residues: 671 helix: 0.70 (0.63), residues: 79 sheet: 0.47 (0.35), residues: 217 loop : -0.99 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.015 0.001 TYR C 96 PHE 0.023 0.002 PHE A 69 TRP 0.006 0.001 TRP C 158 HIS 0.003 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 5310) covalent geometry : angle 0.54192 / 0.28 ( 7235) SS BOND : bond 0.00375 / 0.19 ( 4) SS BOND : angle 1.68585 / 0.96 ( 8) hydrogen bonds : bond 0.02795 / 1.91 ( 169) hydrogen bonds : angle 5.42236 / 3.89 ( 483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 36 time to evaluate : 0.124 Fit side-chains REVERT: A 28 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6956 (m-30) REVERT: A 291 ASN cc_start: 0.5893 (OUTLIER) cc_final: 0.5438 (p0) outliers start: 23 outliers final: 17 residues processed: 54 average time/residue: 0.0772 time to fit residues: 5.4886 Evaluate side-chains 54 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 191 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 66 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.190944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.155160 restraints weight = 6557.689| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.46 r_work: 0.3735 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5314 Z= 0.147 Angle : 0.590 7.864 7243 Z= 0.302 Chirality : 0.045 0.161 828 Planarity : 0.005 0.060 934 Dihedral : 5.702 54.777 732 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.47 % Favored : 95.23 % Rotamer: Outliers : 4.00 % Allowed : 25.91 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.56 (0.33), residues: 671 helix: 0.44 (0.62), residues: 80 sheet: 0.40 (0.35), residues: 217 loop : -1.04 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 91 TYR 0.018 0.001 TYR C 96 PHE 0.019 0.002 PHE A 69 TRP 0.009 0.001 TRP D 35 HIS 0.003 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 5310) covalent geometry : angle 0.58598 / 0.30 ( 7235) SS BOND : bond 0.00583 / 0.29 ( 4) SS BOND : angle 2.24991 / 1.29 ( 8) hydrogen bonds : bond 0.03177 / 2.19 ( 169) hydrogen bonds : angle 5.72839 / 4.13 ( 483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 36 time to evaluate : 0.208 Fit side-chains REVERT: A 21 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: A 28 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6993 (m-30) REVERT: A 64 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7469 (m-30) REVERT: A 291 ASN cc_start: 0.5891 (OUTLIER) cc_final: 0.5514 (p0) outliers start: 23 outliers final: 16 residues processed: 56 average time/residue: 0.0547 time to fit residues: 4.1938 Evaluate side-chains 55 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 35 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 0.0050 chunk 28 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.192336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.156565 restraints weight = 6623.929| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.50 r_work: 0.3749 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5314 Z= 0.118 Angle : 0.559 7.923 7243 Z= 0.286 Chirality : 0.044 0.160 828 Planarity : 0.005 0.060 934 Dihedral : 5.586 55.310 732 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.43 % Favored : 96.27 % Rotamer: Outliers : 4.17 % Allowed : 25.74 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.53 (0.33), residues: 671 helix: 0.54 (0.62), residues: 80 sheet: 0.39 (0.35), residues: 217 loop : -1.02 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.014 0.001 TYR C 96 PHE 0.022 0.002 PHE A 69 TRP 0.006 0.001 TRP A 59 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 5310) covalent geometry : angle 0.55497 / 0.28 ( 7235) SS BOND : bond 0.00441 / 0.22 ( 4) SS BOND : angle 2.12968 / 1.20 ( 8) hydrogen bonds : bond 0.02873 / 1.96 ( 169) hydrogen bonds : angle 5.56216 / 3.99 ( 483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 35 time to evaluate : 0.152 Fit side-chains REVERT: A 21 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: A 28 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6993 (m-30) REVERT: A 64 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: A 291 ASN cc_start: 0.5825 (OUTLIER) cc_final: 0.5299 (p0) outliers start: 24 outliers final: 17 residues processed: 54 average time/residue: 0.0601 time to fit residues: 4.3621 Evaluate side-chains 57 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 2 optimal weight: 0.0670 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.194511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.158128 restraints weight = 6668.424| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.52 r_work: 0.3775 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5314 Z= 0.096 Angle : 0.541 7.826 7243 Z= 0.275 Chirality : 0.043 0.157 828 Planarity : 0.005 0.058 934 Dihedral : 5.414 54.975 732 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.58 % Favored : 96.13 % Rotamer: Outliers : 3.65 % Allowed : 26.26 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.44 (0.33), residues: 671 helix: 0.69 (0.63), residues: 80 sheet: 0.32 (0.34), residues: 227 loop : -0.91 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 103 TYR 0.012 0.001 TYR C 96 PHE 0.023 0.001 PHE A 69 TRP 0.006 0.001 TRP A 59 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 5310) covalent geometry : angle 0.53817 / 0.27 ( 7235) SS BOND : bond 0.00365 / 0.18 ( 4) SS BOND : angle 1.80856 / 1.00 ( 8) hydrogen bonds : bond 0.02611 / 1.78 ( 169) hydrogen bonds : angle 5.39233 / 3.86 ( 483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1244.49 seconds wall clock time: 22 minutes 1.71 seconds (1321.71 seconds total)