Starting phenix.real_space_refine on Wed Jun 4 17:58:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3n_38892/06_2025/8y3n_38892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3n_38892/06_2025/8y3n_38892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3n_38892/06_2025/8y3n_38892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3n_38892/06_2025/8y3n_38892.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3n_38892/06_2025/8y3n_38892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3n_38892/06_2025/8y3n_38892.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.026 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 16 5.16 5 C 2321 2.51 5 N 633 2.21 5 O 724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3694 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 917 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Chain: "B" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 939 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 925 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Chain: "D" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 913 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.14, per 1000 atoms: 0.85 Number of scatterers: 3694 At special positions: 0 Unit cell: (70.3, 94.05, 86.45, 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 16 16.00 O 724 8.00 N 633 7.00 C 2321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.88 Conformation dependent library (CDL) restraints added in 444.9 milliseconds 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 932 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 5 sheets defined 20.9% alpha, 42.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 97 through 113 removed outlier: 3.566A pdb=" N CYS A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 removed outlier: 3.620A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.500A pdb=" N LEU B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 124 Processing helix chain 'C' and resid 97 through 112 removed outlier: 3.771A pdb=" N CYS C 101 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 125 Processing helix chain 'D' and resid 97 through 112 Processing helix chain 'D' and resid 116 through 125 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 3.547A pdb=" N PHE A 7 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 20 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE A 33 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 26 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 84 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TRP A 82 " --> pdb=" O LYS A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 8 removed outlier: 3.547A pdb=" N PHE A 7 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 20 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE A 33 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 26 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 90 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 60 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 62 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU B 89 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU A 89 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN B 87 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ARG B 83 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA B 80 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ALA B 68 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TRP B 82 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 66 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 64 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 62 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 46 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B 25 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLU B 31 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 18 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 7 through 10 removed outlier: 6.736A pdb=" N VAL C 18 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU C 31 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE C 25 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA C 46 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C 59 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 64 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 84 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP C 82 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 7 through 10 removed outlier: 6.736A pdb=" N VAL C 18 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU C 31 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE C 25 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA C 46 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C 59 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU D 89 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 89 " --> pdb=" O ASN D 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 21 through 26 removed outlier: 7.003A pdb=" N GLU D 31 " --> pdb=" O SER D 23 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE D 25 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA D 46 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 44 " --> pdb=" O TRP D 32 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 492 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: 0.88 Time building geometry restraints manager: 1.06 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: 1203 1.34 - 1.45: 534 1.45 - 1.57: 1995 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3756 Sorted by residual: bond pdb=" CG ASN A 12 " pdb=" OD1 ASN A 12 " ideal model delta sigma weight residual 1.231 1.328 -0.097 1.90e-02 2.77e+03 2.63e+01 bond pdb=" CG ASN D 87 " pdb=" OD1 ASN D 87 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.50e+01 bond pdb=" CG ASN C 116 " pdb=" ND2 ASN C 116 " ideal model delta sigma weight residual 1.328 1.227 0.101 2.10e-02 2.27e+03 2.30e+01 bond pdb=" CG ASN D 87 " pdb=" ND2 ASN D 87 " ideal model delta sigma weight residual 1.328 1.230 0.098 2.10e-02 2.27e+03 2.17e+01 bond pdb=" CG ASN A 12 " pdb=" ND2 ASN A 12 " ideal model delta sigma weight residual 1.328 1.230 0.098 2.10e-02 2.27e+03 2.16e+01 ... (remaining 3751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 4729 1.34 - 2.69: 298 2.69 - 4.03: 59 4.03 - 5.38: 24 5.38 - 6.72: 7 Bond angle restraints: 5117 Sorted by residual: angle pdb=" C MET A 108 " pdb=" N GLN A 109 " pdb=" CA GLN A 109 " ideal model delta sigma weight residual 120.28 115.24 5.04 1.34e+00 5.57e-01 1.41e+01 angle pdb=" N GLU D 31 " pdb=" CA GLU D 31 " pdb=" C GLU D 31 " ideal model delta sigma weight residual 107.49 113.99 -6.50 1.74e+00 3.30e-01 1.40e+01 angle pdb=" N GLU B 102 " pdb=" CA GLU B 102 " pdb=" C GLU B 102 " ideal model delta sigma weight residual 111.28 107.34 3.94 1.09e+00 8.42e-01 1.31e+01 angle pdb=" CB ASN C 116 " pdb=" CG ASN C 116 " pdb=" ND2 ASN C 116 " ideal model delta sigma weight residual 116.40 121.36 -4.96 1.50e+00 4.44e-01 1.09e+01 angle pdb=" CA GLN C 54 " pdb=" CB GLN C 54 " pdb=" CG GLN C 54 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.87e+00 ... (remaining 5112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.07: 2001 14.07 - 28.13: 188 28.13 - 42.20: 59 42.20 - 56.27: 14 56.27 - 70.33: 3 Dihedral angle restraints: 2265 sinusoidal: 833 harmonic: 1432 Sorted by residual: dihedral pdb=" CA SER D 52 " pdb=" C SER D 52 " pdb=" N ALA D 53 " pdb=" CA ALA D 53 " ideal model delta harmonic sigma weight residual 180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLN C 50 " pdb=" C GLN C 50 " pdb=" N SER C 51 " pdb=" CA SER C 51 " ideal model delta harmonic sigma weight residual -180.00 -161.06 -18.94 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA SER A 126 " pdb=" C SER A 126 " pdb=" N GLY A 127 " pdb=" CA GLY A 127 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 328 0.032 - 0.063: 173 0.063 - 0.094: 63 0.094 - 0.126: 39 0.126 - 0.157: 7 Chirality restraints: 610 Sorted by residual: chirality pdb=" CA PRO C 117 " pdb=" N PRO C 117 " pdb=" C PRO C 117 " pdb=" CB PRO C 117 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA PRO B 117 " pdb=" N PRO B 117 " pdb=" C PRO B 117 " pdb=" CB PRO B 117 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE C 60 " pdb=" N ILE C 60 " pdb=" C ILE C 60 " pdb=" CB ILE C 60 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 607 not shown) Planarity restraints: 659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 116 " 0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO B 117 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 117 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 117 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 107 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C ALA D 107 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA D 107 " 0.012 2.00e-02 2.50e+03 pdb=" N MET D 108 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 116 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO D 117 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 117 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 117 " 0.025 5.00e-02 4.00e+02 ... (remaining 656 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 1463 2.89 - 3.39: 3453 3.39 - 3.89: 5627 3.89 - 4.40: 5947 4.40 - 4.90: 10962 Nonbonded interactions: 27452 Sorted by model distance: nonbonded pdb=" OD1 ASN C 24 " pdb=" N PHE C 25 " model vdw 2.382 3.120 nonbonded pdb=" O TYR D 58 " pdb=" OG1 THR D 59 " model vdw 2.387 3.040 nonbonded pdb=" NH1 ARG A 56 " pdb=" O ASN B 125 " model vdw 2.398 3.120 nonbonded pdb=" ND2 ASN C 12 " pdb=" O GLY C 16 " model vdw 2.399 3.120 nonbonded pdb=" NE2 GLN A 109 " pdb=" O LEU B 112 " model vdw 2.404 3.120 ... (remaining 27447 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 112 or (resid 113 and (name N or name CA or name \ C or name O or name CB )) or resid 114 through 128)) selection = (chain 'B' and (resid 2 through 71 or resid 77 through 112 or (resid 113 and (na \ me N or name CA or name C or name O or name CB )) or resid 114 through 128)) selection = (chain 'C' and (resid 2 through 112 or (resid 113 and (name N or name CA or name \ C or name O or name CB )) or resid 114 through 128)) selection = (chain 'D' and resid 2 through 128) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.550 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.007 0.101 3756 Z= 0.344 Angle : 0.820 6.721 5117 Z= 0.469 Chirality : 0.048 0.157 610 Planarity : 0.006 0.058 659 Dihedral : 13.357 70.333 1333 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.37), residues: 478 helix: 0.28 (0.52), residues: 101 sheet: -2.52 (0.38), residues: 159 loop : -2.64 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 32 PHE 0.028 0.003 PHE D 4 TYR 0.012 0.002 TYR B 42 ARG 0.009 0.001 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.16791 ( 150) hydrogen bonds : angle 7.59665 ( 492) covalent geometry : bond 0.00726 ( 3756) covalent geometry : angle 0.82013 ( 5117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.466 Fit side-chains REVERT: C 27 ASN cc_start: 0.7206 (t0) cc_final: 0.6970 (t0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1295 time to fit residues: 12.9047 Evaluate side-chains 60 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN D 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.150561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120911 restraints weight = 4516.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122195 restraints weight = 3782.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122195 restraints weight = 3377.657| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3756 Z= 0.152 Angle : 0.648 9.273 5117 Z= 0.334 Chirality : 0.046 0.133 610 Planarity : 0.005 0.042 659 Dihedral : 5.728 52.500 518 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.99 % Allowed : 9.36 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.38), residues: 478 helix: 0.70 (0.51), residues: 102 sheet: -2.01 (0.41), residues: 161 loop : -2.30 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 32 PHE 0.019 0.002 PHE D 4 TYR 0.008 0.001 TYR B 42 ARG 0.003 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 150) hydrogen bonds : angle 5.38222 ( 492) covalent geometry : bond 0.00355 ( 3756) covalent geometry : angle 0.64849 ( 5117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.410 Fit side-chains REVERT: A 40 GLN cc_start: 0.8703 (tp40) cc_final: 0.8359 (tp-100) outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.1135 time to fit residues: 10.1640 Evaluate side-chains 56 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 4 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN C 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.148390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119628 restraints weight = 4527.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120875 restraints weight = 3888.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121482 restraints weight = 3525.517| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3756 Z= 0.204 Angle : 0.658 7.036 5117 Z= 0.341 Chirality : 0.046 0.139 610 Planarity : 0.006 0.076 659 Dihedral : 5.870 59.889 518 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 1.23 % Allowed : 13.55 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.38), residues: 478 helix: 0.87 (0.50), residues: 101 sheet: -1.84 (0.42), residues: 161 loop : -2.29 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 32 PHE 0.018 0.002 PHE D 4 TYR 0.014 0.002 TYR D 85 ARG 0.003 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 150) hydrogen bonds : angle 5.10464 ( 492) covalent geometry : bond 0.00487 ( 3756) covalent geometry : angle 0.65792 ( 5117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.368 Fit side-chains REVERT: A 40 GLN cc_start: 0.8709 (tp40) cc_final: 0.8494 (tp-100) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.1206 time to fit residues: 9.7347 Evaluate side-chains 57 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.151260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121277 restraints weight = 4469.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122777 restraints weight = 3711.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123953 restraints weight = 3270.752| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3756 Z= 0.135 Angle : 0.601 7.933 5117 Z= 0.310 Chirality : 0.045 0.143 610 Planarity : 0.005 0.074 659 Dihedral : 5.696 63.651 518 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.72 % Allowed : 16.26 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.39), residues: 478 helix: 1.08 (0.50), residues: 101 sheet: -1.63 (0.42), residues: 164 loop : -2.16 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 32 PHE 0.013 0.002 PHE C 4 TYR 0.014 0.001 TYR D 85 ARG 0.002 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 150) hydrogen bonds : angle 4.77121 ( 492) covalent geometry : bond 0.00314 ( 3756) covalent geometry : angle 0.60133 ( 5117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.411 Fit side-chains REVERT: A 6 GLN cc_start: 0.8793 (pp30) cc_final: 0.8351 (pp30) REVERT: A 40 GLN cc_start: 0.8655 (tp40) cc_final: 0.8418 (tp-100) REVERT: B 27 ASN cc_start: 0.7537 (t0) cc_final: 0.7317 (t0) REVERT: D 125 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7303 (m110) outliers start: 7 outliers final: 5 residues processed: 60 average time/residue: 0.0964 time to fit residues: 8.0883 Evaluate side-chains 56 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 125 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.150098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120645 restraints weight = 4570.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121900 restraints weight = 3839.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123271 restraints weight = 3420.695| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3756 Z= 0.165 Angle : 0.606 7.649 5117 Z= 0.312 Chirality : 0.045 0.141 610 Planarity : 0.005 0.077 659 Dihedral : 5.829 72.125 518 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.46 % Allowed : 17.98 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.39), residues: 478 helix: 1.15 (0.51), residues: 101 sheet: -1.48 (0.42), residues: 159 loop : -2.18 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 32 PHE 0.013 0.002 PHE C 4 TYR 0.012 0.001 TYR D 85 ARG 0.002 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 150) hydrogen bonds : angle 4.61541 ( 492) covalent geometry : bond 0.00390 ( 3756) covalent geometry : angle 0.60555 ( 5117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.365 Fit side-chains REVERT: A 6 GLN cc_start: 0.8816 (pp30) cc_final: 0.8378 (pp30) REVERT: B 27 ASN cc_start: 0.7568 (t0) cc_final: 0.7347 (t0) REVERT: D 125 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.7238 (m110) outliers start: 10 outliers final: 5 residues processed: 60 average time/residue: 0.1079 time to fit residues: 8.8791 Evaluate side-chains 56 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 125 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 10.0000 chunk 37 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 44 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.154862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122452 restraints weight = 4480.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124903 restraints weight = 3312.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126743 restraints weight = 2745.612| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3756 Z= 0.107 Angle : 0.556 7.594 5117 Z= 0.287 Chirality : 0.044 0.132 610 Planarity : 0.005 0.076 659 Dihedral : 5.694 77.597 518 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.97 % Allowed : 18.72 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.39), residues: 478 helix: 1.32 (0.50), residues: 101 sheet: -1.31 (0.42), residues: 164 loop : -1.94 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 32 PHE 0.012 0.002 PHE C 4 TYR 0.012 0.001 TYR D 85 ARG 0.003 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 150) hydrogen bonds : angle 4.37847 ( 492) covalent geometry : bond 0.00237 ( 3756) covalent geometry : angle 0.55636 ( 5117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.375 Fit side-chains REVERT: A 6 GLN cc_start: 0.8811 (pp30) cc_final: 0.8360 (pp30) REVERT: A 40 GLN cc_start: 0.8650 (tp40) cc_final: 0.8389 (tp-100) REVERT: B 27 ASN cc_start: 0.7603 (t0) cc_final: 0.7351 (t0) REVERT: D 82 TRP cc_start: 0.8650 (p-90) cc_final: 0.8304 (p90) REVERT: D 125 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.7056 (m110) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.1037 time to fit residues: 8.9823 Evaluate side-chains 60 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 125 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.153077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122292 restraints weight = 4431.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124246 restraints weight = 3441.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.125769 restraints weight = 2932.896| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3756 Z= 0.135 Angle : 0.573 8.071 5117 Z= 0.296 Chirality : 0.044 0.128 610 Planarity : 0.005 0.078 659 Dihedral : 5.842 83.010 518 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.22 % Allowed : 18.97 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.39), residues: 478 helix: 1.34 (0.50), residues: 101 sheet: -1.30 (0.42), residues: 164 loop : -1.96 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 32 PHE 0.011 0.002 PHE C 4 TYR 0.010 0.001 TYR D 42 ARG 0.003 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 150) hydrogen bonds : angle 4.34372 ( 492) covalent geometry : bond 0.00319 ( 3756) covalent geometry : angle 0.57273 ( 5117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.392 Fit side-chains REVERT: A 6 GLN cc_start: 0.8844 (pp30) cc_final: 0.8366 (pp30) REVERT: A 40 GLN cc_start: 0.8658 (tp40) cc_final: 0.8374 (tp-100) REVERT: B 27 ASN cc_start: 0.7580 (t0) cc_final: 0.7316 (t0) outliers start: 9 outliers final: 7 residues processed: 60 average time/residue: 0.1716 time to fit residues: 14.4702 Evaluate side-chains 62 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 40 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 overall best weight: 1.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN D 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121569 restraints weight = 4461.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123850 restraints weight = 3405.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125281 restraints weight = 2837.134| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3756 Z= 0.140 Angle : 0.578 8.034 5117 Z= 0.297 Chirality : 0.044 0.129 610 Planarity : 0.005 0.081 659 Dihedral : 6.015 89.751 518 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.71 % Allowed : 20.20 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.39), residues: 478 helix: 1.42 (0.50), residues: 101 sheet: -1.26 (0.42), residues: 164 loop : -1.96 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 32 PHE 0.011 0.002 PHE C 4 TYR 0.008 0.001 TYR D 42 ARG 0.002 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 150) hydrogen bonds : angle 4.32283 ( 492) covalent geometry : bond 0.00329 ( 3756) covalent geometry : angle 0.57802 ( 5117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.374 Fit side-chains REVERT: A 6 GLN cc_start: 0.8872 (pp30) cc_final: 0.8438 (pp30) REVERT: A 40 GLN cc_start: 0.8675 (tp40) cc_final: 0.8436 (tp-100) REVERT: B 27 ASN cc_start: 0.7663 (t0) cc_final: 0.7413 (t0) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.0960 time to fit residues: 8.8010 Evaluate side-chains 66 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.150252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118821 restraints weight = 4539.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120941 restraints weight = 3452.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122277 restraints weight = 2922.575| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3756 Z= 0.186 Angle : 0.628 8.213 5117 Z= 0.322 Chirality : 0.045 0.140 610 Planarity : 0.006 0.082 659 Dihedral : 6.117 87.167 518 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 1.97 % Allowed : 20.69 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.39), residues: 478 helix: 1.45 (0.50), residues: 101 sheet: -1.34 (0.42), residues: 168 loop : -2.05 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 32 PHE 0.021 0.002 PHE D 95 TYR 0.008 0.001 TYR D 42 ARG 0.002 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 150) hydrogen bonds : angle 4.43772 ( 492) covalent geometry : bond 0.00445 ( 3756) covalent geometry : angle 0.62810 ( 5117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.430 Fit side-chains REVERT: A 6 GLN cc_start: 0.8904 (pp30) cc_final: 0.8478 (pp30) REVERT: A 40 GLN cc_start: 0.8694 (tp40) cc_final: 0.8426 (tp-100) REVERT: B 27 ASN cc_start: 0.7736 (t0) cc_final: 0.7497 (t0) outliers start: 8 outliers final: 8 residues processed: 57 average time/residue: 0.0974 time to fit residues: 7.7695 Evaluate side-chains 60 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122528 restraints weight = 4461.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124896 restraints weight = 3366.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126144 restraints weight = 2807.384| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3756 Z= 0.120 Angle : 0.568 8.191 5117 Z= 0.293 Chirality : 0.044 0.128 610 Planarity : 0.005 0.081 659 Dihedral : 5.864 85.881 518 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.97 % Allowed : 21.43 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.39), residues: 478 helix: 1.64 (0.50), residues: 101 sheet: -1.19 (0.41), residues: 180 loop : -1.90 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 32 PHE 0.023 0.002 PHE D 95 TYR 0.007 0.001 TYR D 42 ARG 0.002 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 150) hydrogen bonds : angle 4.24174 ( 492) covalent geometry : bond 0.00277 ( 3756) covalent geometry : angle 0.56780 ( 5117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.402 Fit side-chains REVERT: A 6 GLN cc_start: 0.8866 (pp30) cc_final: 0.8452 (pp30) REVERT: A 40 GLN cc_start: 0.8678 (tp40) cc_final: 0.8466 (tp-100) REVERT: B 27 ASN cc_start: 0.7696 (t0) cc_final: 0.7492 (t0) outliers start: 8 outliers final: 8 residues processed: 63 average time/residue: 0.1075 time to fit residues: 9.4405 Evaluate side-chains 63 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125020 restraints weight = 4430.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127204 restraints weight = 3437.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128795 restraints weight = 2902.412| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3756 Z= 0.109 Angle : 0.560 8.199 5117 Z= 0.288 Chirality : 0.044 0.128 610 Planarity : 0.005 0.080 659 Dihedral : 5.725 84.221 518 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.48 % Allowed : 22.66 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.39), residues: 478 helix: 1.73 (0.49), residues: 99 sheet: -1.17 (0.41), residues: 170 loop : -1.81 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 32 PHE 0.023 0.002 PHE D 95 TYR 0.006 0.001 TYR D 42 ARG 0.002 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 150) hydrogen bonds : angle 4.19626 ( 492) covalent geometry : bond 0.00250 ( 3756) covalent geometry : angle 0.56042 ( 5117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1359.65 seconds wall clock time: 24 minutes 26.75 seconds (1466.75 seconds total)