Starting phenix.real_space_refine on Thu Mar 6 09:05:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cio_16683/03_2025/8cio_16683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cio_16683/03_2025/8cio_16683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cio_16683/03_2025/8cio_16683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cio_16683/03_2025/8cio_16683.map" model { file = "/net/cci-nas-00/data/ceres_data/8cio_16683/03_2025/8cio_16683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cio_16683/03_2025/8cio_16683.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3485 2.51 5 N 965 2.21 5 O 1185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5655 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1131 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.84, per 1000 atoms: 0.50 Number of scatterers: 5655 At special positions: 0 Unit cell: (64.428, 64.428, 219.492, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1185 8.00 N 965 7.00 C 3485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 85 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 85 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 85 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 85 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 85 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 711.5 milliseconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1390 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 Processing sheet with id=AA2, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY B 76 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY B 76 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ASP B 71 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY B 61 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN B 73 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP B 59 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLN A 34 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N SER B 62 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL A 36 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 170 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY A 76 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY A 76 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ASP A 71 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 61 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN A 73 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP A 59 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL D 36 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A 62 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA7, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.616A pdb=" N SER A 102 " --> pdb=" O GLN A 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 105 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 29 Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 80 removed outlier: 3.684A pdb=" N GLY C 76 " --> pdb=" O GLY C 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 79 through 80 removed outlier: 3.684A pdb=" N GLY C 76 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ASP C 71 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY C 61 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLN C 73 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP C 59 " --> pdb=" O GLN C 73 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N GLN B 34 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER C 62 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 36 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 170 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.616A pdb=" N SER B 102 " --> pdb=" O GLN B 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 105 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.615A pdb=" N SER C 102 " --> pdb=" O GLN C 105 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 105 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY D 76 " --> pdb=" O GLY D 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 79 through 80 removed outlier: 3.683A pdb=" N GLY D 76 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ASP D 71 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY D 61 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLN D 73 " --> pdb=" O ASP D 59 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP D 59 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL E 36 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER D 62 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY D 170 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 95 Processing sheet with id=AB7, first strand: chain 'D' and resid 101 through 102 removed outlier: 3.615A pdb=" N SER D 102 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN D 105 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 57 through 58 removed outlier: 3.684A pdb=" N GLY E 76 " --> pdb=" O GLY E 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 57 through 58 Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 95 Processing sheet with id=AC2, first strand: chain 'E' and resid 101 through 102 removed outlier: 3.616A pdb=" N SER E 102 " --> pdb=" O GLN E 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN E 105 " --> pdb=" O SER E 102 " (cutoff:3.500A) 132 hydrogen bonds defined for protein. 264 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1905 1.34 - 1.46: 1123 1.46 - 1.57: 2682 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 5740 Sorted by residual: bond pdb=" CA THR E 77 " pdb=" CB THR E 77 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.69e-02 3.50e+03 8.22e-01 bond pdb=" CA THR C 77 " pdb=" CB THR C 77 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.85e-01 bond pdb=" CA THR B 77 " pdb=" CB THR B 77 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.56e-01 bond pdb=" CA THR A 77 " pdb=" CB THR A 77 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.49e-01 bond pdb=" CB ASP C 125 " pdb=" CG ASP C 125 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.43e-01 ... (remaining 5735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 7712 1.40 - 2.80: 135 2.80 - 4.20: 33 4.20 - 5.59: 5 5.59 - 6.99: 5 Bond angle restraints: 7890 Sorted by residual: angle pdb=" CA THR D 77 " pdb=" CB THR D 77 " pdb=" CG2 THR D 77 " ideal model delta sigma weight residual 110.50 114.10 -3.60 1.70e+00 3.46e-01 4.48e+00 angle pdb=" CA THR A 77 " pdb=" CB THR A 77 " pdb=" CG2 THR A 77 " ideal model delta sigma weight residual 110.50 114.07 -3.57 1.70e+00 3.46e-01 4.41e+00 angle pdb=" CA THR B 77 " pdb=" CB THR B 77 " pdb=" CG2 THR B 77 " ideal model delta sigma weight residual 110.50 114.06 -3.56 1.70e+00 3.46e-01 4.40e+00 angle pdb=" CA THR C 77 " pdb=" CB THR C 77 " pdb=" CG2 THR C 77 " ideal model delta sigma weight residual 110.50 114.06 -3.56 1.70e+00 3.46e-01 4.39e+00 angle pdb=" CA THR E 77 " pdb=" CB THR E 77 " pdb=" CG2 THR E 77 " ideal model delta sigma weight residual 110.50 114.06 -3.56 1.70e+00 3.46e-01 4.39e+00 ... (remaining 7885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.25: 2845 10.25 - 20.51: 305 20.51 - 30.76: 125 30.76 - 41.02: 45 41.02 - 51.27: 15 Dihedral angle restraints: 3335 sinusoidal: 1130 harmonic: 2205 Sorted by residual: dihedral pdb=" CA GLN B 133 " pdb=" CB GLN B 133 " pdb=" CG GLN B 133 " pdb=" CD GLN B 133 " ideal model delta sinusoidal sigma weight residual 180.00 133.78 46.22 3 1.50e+01 4.44e-03 8.30e+00 dihedral pdb=" CA GLN C 133 " pdb=" CB GLN C 133 " pdb=" CG GLN C 133 " pdb=" CD GLN C 133 " ideal model delta sinusoidal sigma weight residual 180.00 133.79 46.21 3 1.50e+01 4.44e-03 8.30e+00 dihedral pdb=" CA GLN A 133 " pdb=" CB GLN A 133 " pdb=" CG GLN A 133 " pdb=" CD GLN A 133 " ideal model delta sinusoidal sigma weight residual 180.00 133.80 46.20 3 1.50e+01 4.44e-03 8.30e+00 ... (remaining 3332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 630 0.032 - 0.063: 204 0.063 - 0.095: 72 0.095 - 0.127: 84 0.127 - 0.159: 15 Chirality restraints: 1005 Sorted by residual: chirality pdb=" CB THR D 77 " pdb=" CA THR D 77 " pdb=" OG1 THR D 77 " pdb=" CG2 THR D 77 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CB THR A 77 " pdb=" CA THR A 77 " pdb=" OG1 THR A 77 " pdb=" CG2 THR A 77 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CB THR B 77 " pdb=" CA THR B 77 " pdb=" OG1 THR B 77 " pdb=" CG2 THR B 77 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 1002 not shown) Planarity restraints: 1015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 151 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO B 152 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 152 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 152 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 151 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO E 152 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO E 152 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 152 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 151 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO C 152 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " 0.014 5.00e-02 4.00e+02 ... (remaining 1012 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 2489 2.91 - 3.41: 5100 3.41 - 3.91: 8534 3.91 - 4.40: 9411 4.40 - 4.90: 16364 Nonbonded interactions: 41898 Sorted by model distance: nonbonded pdb=" O SER E 144 " pdb=" OG1 THR E 145 " model vdw 2.418 3.040 nonbonded pdb=" O SER C 144 " pdb=" OG1 THR C 145 " model vdw 2.418 3.040 nonbonded pdb=" O SER D 144 " pdb=" OG1 THR D 145 " model vdw 2.418 3.040 nonbonded pdb=" O SER B 144 " pdb=" OG1 THR B 145 " model vdw 2.418 3.040 nonbonded pdb=" O SER A 144 " pdb=" OG1 THR A 145 " model vdw 2.419 3.040 ... (remaining 41893 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.500 Find NCS groups from input model: 0.120 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.002 0.023 5740 Z= 0.156 Angle : 0.547 6.992 7890 Z= 0.284 Chirality : 0.048 0.159 1005 Planarity : 0.003 0.026 1015 Dihedral : 11.522 51.274 1930 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.30), residues: 785 helix: None (None), residues: 0 sheet: 1.41 (0.47), residues: 135 loop : -1.80 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 55 HIS 0.002 0.001 HIS D 100 PHE 0.004 0.001 PHE C 60 TYR 0.006 0.001 TYR B 120 ARG 0.002 0.000 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.557 Fit side-chains REVERT: A 165 PRO cc_start: 0.7375 (Cg_exo) cc_final: 0.7134 (Cg_endo) REVERT: B 84 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8501 (tm-30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1039 time to fit residues: 17.9418 Evaluate side-chains 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.0670 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.3200 r_free = 0.3200 target = 0.090600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.078340 restraints weight = 11719.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.080888 restraints weight = 6637.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.082638 restraints weight = 4438.903| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5740 Z= 0.224 Angle : 0.581 8.907 7890 Z= 0.301 Chirality : 0.049 0.146 1005 Planarity : 0.003 0.028 1015 Dihedral : 4.099 17.141 835 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 1.59 % Allowed : 11.11 % Favored : 87.30 % 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: -1.63 (0.30), residues: 785 helix: None (None), residues: 0 sheet: 1.33 (0.46), residues: 135 loop : -1.81 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 182 HIS 0.003 0.001 HIS D 63 PHE 0.009 0.002 PHE C 60 TYR 0.020 0.001 TYR D 107 ARG 0.002 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.576 Fit side-chains REVERT: D 108 MET cc_start: 0.7952 (mtt) cc_final: 0.7726 (mtp) outliers start: 10 outliers final: 8 residues processed: 94 average time/residue: 0.1066 time to fit residues: 15.0642 Evaluate side-chains 82 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.086916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.074021 restraints weight = 12118.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.076729 restraints weight = 6547.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.078600 restraints weight = 4284.704| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5740 Z= 0.191 Angle : 0.592 14.216 7890 Z= 0.289 Chirality : 0.049 0.139 1005 Planarity : 0.003 0.028 1015 Dihedral : 4.012 17.841 835 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.17 % Allowed : 13.33 % Favored : 83.49 % 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: -1.65 (0.30), residues: 785 helix: None (None), residues: 0 sheet: 1.37 (0.46), residues: 135 loop : -1.84 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 55 HIS 0.002 0.001 HIS D 63 PHE 0.006 0.001 PHE C 60 TYR 0.007 0.001 TYR D 107 ARG 0.001 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.558 Fit side-chains REVERT: B 84 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8418 (tm-30) outliers start: 20 outliers final: 13 residues processed: 101 average time/residue: 0.0990 time to fit residues: 15.1895 Evaluate side-chains 88 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 177 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 0.0170 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.089452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077211 restraints weight = 11992.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.079748 restraints weight = 6740.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.081499 restraints weight = 4496.976| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5740 Z= 0.222 Angle : 0.617 14.234 7890 Z= 0.299 Chirality : 0.049 0.139 1005 Planarity : 0.003 0.027 1015 Dihedral : 4.146 21.084 835 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.81 % Favored : 89.68 % Rotamer: Outliers : 3.65 % Allowed : 15.08 % Favored : 81.27 % 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: -1.66 (0.30), residues: 785 helix: None (None), residues: 0 sheet: 1.27 (0.45), residues: 135 loop : -1.82 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 55 HIS 0.002 0.001 HIS D 63 PHE 0.008 0.001 PHE C 60 TYR 0.006 0.001 TYR D 123 ARG 0.002 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.572 Fit side-chains REVERT: B 84 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8473 (tp40) REVERT: E 141 SER cc_start: 0.8382 (t) cc_final: 0.8112 (p) outliers start: 23 outliers final: 17 residues processed: 97 average time/residue: 0.1061 time to fit residues: 15.5992 Evaluate side-chains 90 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.089729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.077534 restraints weight = 11723.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080033 restraints weight = 6586.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.081756 restraints weight = 4396.517| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5740 Z= 0.246 Angle : 0.630 16.218 7890 Z= 0.307 Chirality : 0.049 0.140 1005 Planarity : 0.003 0.027 1015 Dihedral : 4.326 25.081 835 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.81 % Favored : 89.55 % Rotamer: Outliers : 4.13 % Allowed : 16.83 % Favored : 79.05 % 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: -1.72 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.19 (0.45), residues: 135 loop : -1.86 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 182 HIS 0.003 0.001 HIS D 63 PHE 0.008 0.001 PHE C 60 TYR 0.008 0.001 TYR B 172 ARG 0.002 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.561 Fit side-chains REVERT: E 141 SER cc_start: 0.8396 (t) cc_final: 0.8121 (p) outliers start: 26 outliers final: 18 residues processed: 98 average time/residue: 0.0987 time to fit residues: 14.7887 Evaluate side-chains 89 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 0.0670 chunk 46 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.074502 restraints weight = 11989.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077177 restraints weight = 6467.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.079021 restraints weight = 4220.039| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.002 0.032 5740 Z= 0.163 Angle : 0.611 15.957 7890 Z= 0.292 Chirality : 0.048 0.137 1005 Planarity : 0.003 0.027 1015 Dihedral : 3.945 21.255 835 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.04 % Favored : 90.32 % Rotamer: Outliers : 3.02 % Allowed : 18.25 % Favored : 78.73 % 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: -1.69 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.22 (0.45), residues: 135 loop : -1.83 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 182 HIS 0.002 0.000 HIS E 100 PHE 0.005 0.001 PHE C 60 TYR 0.007 0.001 TYR D 107 ARG 0.001 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.578 Fit side-chains REVERT: B 121 ASN cc_start: 0.7251 (m110) cc_final: 0.7041 (t0) outliers start: 19 outliers final: 14 residues processed: 96 average time/residue: 0.1007 time to fit residues: 14.6736 Evaluate side-chains 85 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 71 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 72 optimal weight: 0.0770 chunk 50 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.087870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.075059 restraints weight = 11952.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.077753 restraints weight = 6407.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.079623 restraints weight = 4162.834| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 5740 Z= 0.205 Angle : 0.652 16.270 7890 Z= 0.314 Chirality : 0.049 0.215 1005 Planarity : 0.003 0.028 1015 Dihedral : 3.903 20.250 835 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.55 % Favored : 89.81 % Rotamer: Outliers : 3.02 % Allowed : 19.68 % Favored : 77.30 % 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: -1.75 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.19 (0.45), residues: 135 loop : -1.89 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 182 HIS 0.002 0.001 HIS D 63 PHE 0.005 0.001 PHE C 60 TYR 0.007 0.001 TYR D 107 ARG 0.001 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.600 Fit side-chains REVERT: B 121 ASN cc_start: 0.7256 (m110) cc_final: 0.7019 (t0) outliers start: 19 outliers final: 16 residues processed: 90 average time/residue: 0.1080 time to fit residues: 14.6894 Evaluate side-chains 88 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 32 optimal weight: 0.0270 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 0.0670 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.087683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.074835 restraints weight = 11866.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.077512 restraints weight = 6421.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.079352 restraints weight = 4190.116| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5740 Z= 0.184 Angle : 0.660 15.348 7890 Z= 0.311 Chirality : 0.049 0.137 1005 Planarity : 0.003 0.028 1015 Dihedral : 3.816 19.562 835 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.43 % Favored : 89.94 % Rotamer: Outliers : 3.49 % Allowed : 19.84 % Favored : 76.67 % 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: -1.77 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.19 (0.46), residues: 135 loop : -1.90 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 182 HIS 0.002 0.001 HIS D 63 PHE 0.005 0.001 PHE C 60 TYR 0.007 0.001 TYR D 107 ARG 0.001 0.000 ARG C 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.572 Fit side-chains REVERT: B 121 ASN cc_start: 0.7255 (m110) cc_final: 0.7023 (t0) outliers start: 22 outliers final: 18 residues processed: 95 average time/residue: 0.1033 time to fit residues: 14.9235 Evaluate side-chains 92 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.090426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.077446 restraints weight = 11542.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.080214 restraints weight = 6246.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.082129 restraints weight = 4082.968| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5740 Z= 0.203 Angle : 0.665 15.031 7890 Z= 0.315 Chirality : 0.049 0.196 1005 Planarity : 0.004 0.028 1015 Dihedral : 3.985 23.196 835 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.81 % Favored : 89.55 % Rotamer: Outliers : 3.02 % Allowed : 20.00 % Favored : 76.98 % 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: -1.81 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.15 (0.46), residues: 135 loop : -1.93 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 182 HIS 0.002 0.001 HIS D 63 PHE 0.006 0.001 PHE C 60 TYR 0.009 0.001 TYR E 172 ARG 0.001 0.000 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.561 Fit side-chains REVERT: D 52 ILE cc_start: 0.8427 (mm) cc_final: 0.8197 (mm) REVERT: D 54 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7911 (mm110) outliers start: 19 outliers final: 19 residues processed: 88 average time/residue: 0.1069 time to fit residues: 14.2388 Evaluate side-chains 91 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.0170 chunk 71 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 chunk 26 optimal weight: 0.1980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.092865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.080454 restraints weight = 11542.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.083094 restraints weight = 6513.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.084876 restraints weight = 4335.412| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5740 Z= 0.172 Angle : 0.648 14.864 7890 Z= 0.305 Chirality : 0.049 0.138 1005 Planarity : 0.003 0.027 1015 Dihedral : 3.734 19.432 835 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.55 % Favored : 89.81 % Rotamer: Outliers : 3.17 % Allowed : 19.68 % Favored : 77.14 % 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: -1.78 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.18 (0.46), residues: 135 loop : -1.91 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 55 HIS 0.001 0.000 HIS E 100 PHE 0.005 0.001 PHE C 60 TYR 0.008 0.001 TYR E 172 ARG 0.001 0.000 ARG C 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.645 Fit side-chains REVERT: B 121 ASN cc_start: 0.7267 (m110) cc_final: 0.7040 (t0) REVERT: D 52 ILE cc_start: 0.8292 (mm) cc_final: 0.8082 (mm) REVERT: D 54 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7853 (mm110) outliers start: 20 outliers final: 19 residues processed: 88 average time/residue: 0.1086 time to fit residues: 14.4987 Evaluate side-chains 89 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 chunk 17 optimal weight: 0.0870 chunk 37 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.093955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.081529 restraints weight = 11574.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.084192 restraints weight = 6491.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.086008 restraints weight = 4311.303| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5740 Z= 0.175 Angle : 0.650 14.779 7890 Z= 0.306 Chirality : 0.049 0.174 1005 Planarity : 0.004 0.027 1015 Dihedral : 3.752 21.463 835 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.55 % Favored : 89.81 % Rotamer: Outliers : 3.02 % Allowed : 19.84 % Favored : 77.14 % 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: -1.77 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 1.18 (0.46), residues: 135 loop : -1.90 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 55 HIS 0.001 0.001 HIS E 100 PHE 0.005 0.001 PHE C 60 TYR 0.008 0.001 TYR D 107 ARG 0.001 0.000 ARG D 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1925.55 seconds wall clock time: 34 minutes 16.69 seconds (2056.69 seconds total)