Starting phenix.real_space_refine on Sun Apr 27 12:08:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cio_16683/04_2025/8cio_16683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cio_16683/04_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_16683/04_2025/8cio_16683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cio_16683/04_2025/8cio_16683.map" model { file = "/net/cci-nas-00/data/ceres_data/8cio_16683/04_2025/8cio_16683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cio_16683/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 2.91, per 1000 atoms: 0.51 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: 1.42 Conformation dependent library (CDL) restraints added in 830.0 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: 0.82 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: 1.44 Time building geometry restraints manager: 1.71 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: 1.400 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.030 Find NCS groups from input model: 0.120 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- 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 5745 Z= 0.115 Angle : 0.548 6.992 7900 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 Details of bonding type rmsd hydrogen bonds : bond 0.25275 ( 126) hydrogen bonds : angle 7.76365 ( 264) SS BOND : bond 0.00183 ( 5) SS BOND : angle 1.04394 ( 10) covalent geometry : bond 0.00230 ( 5740) covalent geometry : angle 0.54696 ( 7890) *********************** 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 : 0.586 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: 0.1114 time to fit residues: 19.1247 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 : 0.635 ------------------------------------------------------------------------------- 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 5745 Z= 0.142 Angle : 0.583 8.907 7900 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 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 126) hydrogen bonds : angle 4.96623 ( 264) SS BOND : bond 0.00293 ( 5) SS BOND : angle 1.26362 ( 10) covalent geometry : bond 0.00336 ( 5740) covalent geometry : angle 0.58114 ( 7890) *********************** 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 : 0.645 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: 0.1060 time to fit residues: 15.0533 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 : 0.563 ------------------------------------------------------------------------------- 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 5745 Z= 0.120 Angle : 0.593 14.216 7900 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 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 126) hydrogen bonds : angle 4.43507 ( 264) SS BOND : bond 0.00188 ( 5) SS BOND : angle 1.07345 ( 10) covalent geometry : bond 0.00284 ( 5740) covalent geometry : angle 0.59211 ( 7890) *********************** 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 : 0.583 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: 0.1035 time to fit residues: 15.7986 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 : 0.592 ------------------------------------------------------------------------------- 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 5745 Z= 0.138 Angle : 0.618 14.234 7900 Z= 0.300 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 Details of bonding type rmsd hydrogen bonds : bond 0.02899 ( 126) hydrogen bonds : angle 4.14818 ( 264) SS BOND : bond 0.00282 ( 5) SS BOND : angle 1.16490 ( 10) covalent geometry : bond 0.00332 ( 5740) covalent geometry : angle 0.61701 ( 7890) *********************** 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 : 0.585 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: 0.1174 time to fit residues: 16.9688 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 : 0.531 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.088072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.075849 restraints weight = 11765.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.078334 restraints weight = 6631.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080058 restraints weight = 4446.313| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.006 0.063 5745 Z= 0.225 Angle : 0.688 16.397 7900 Z= 0.342 Chirality : 0.051 0.145 1005 Planarity : 0.004 0.027 1015 Dihedral : 4.909 31.350 835 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.85 % Favored : 87.52 % Rotamer: Outliers : 4.29 % Allowed : 16.67 % 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: -1.86 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.96 (0.45), residues: 135 loop : -1.92 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 182 HIS 0.004 0.002 HIS D 63 PHE 0.011 0.002 PHE C 60 TYR 0.012 0.002 TYR D 123 ARG 0.002 0.000 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 126) hydrogen bonds : angle 4.18995 ( 264) SS BOND : bond 0.00334 ( 5) SS BOND : angle 1.90850 ( 10) covalent geometry : bond 0.00551 ( 5740) covalent geometry : angle 0.68537 ( 7890) *********************** 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: 27 poor density : 76 time to evaluate : 0.615 Fit side-chains REVERT: B 84 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8635 (tp40) outliers start: 27 outliers final: 19 residues processed: 100 average time/residue: 0.1117 time to fit residues: 17.0395 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 : 0.817 ------------------------------------------------------------------------------- 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 166 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 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 Chi-restraints excluded: chain E residue 131 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** B 150 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.087022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.074891 restraints weight = 11808.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.077350 restraints weight = 6697.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.079031 restraints weight = 4494.758| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5745 Z= 0.217 Angle : 0.688 15.733 7900 Z= 0.342 Chirality : 0.051 0.143 1005 Planarity : 0.004 0.028 1015 Dihedral : 4.953 32.173 835 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.46 % Favored : 87.90 % Rotamer: Outliers : 4.29 % Allowed : 17.62 % Favored : 78.10 % 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: -1.99 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.79 (0.44), residues: 135 loop : -1.99 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 182 HIS 0.004 0.002 HIS D 63 PHE 0.009 0.002 PHE C 60 TYR 0.011 0.002 TYR B 172 ARG 0.002 0.000 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 126) hydrogen bonds : angle 4.19669 ( 264) SS BOND : bond 0.00386 ( 5) SS BOND : angle 1.89834 ( 10) covalent geometry : bond 0.00531 ( 5740) covalent geometry : angle 0.68512 ( 7890) *********************** 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 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.655 Fit side-chains REVERT: B 84 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8606 (tp40) REVERT: C 59 ASP cc_start: 0.8314 (t0) cc_final: 0.8106 (t0) outliers start: 27 outliers final: 21 residues processed: 93 average time/residue: 0.1077 time to fit residues: 15.2393 Evaluate side-chains 88 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 75 VAL 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 89 LEU 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 Chi-restraints excluded: chain E residue 131 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 63 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.089923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077289 restraints weight = 11654.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.079965 restraints weight = 6192.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.081812 restraints weight = 4015.615| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5745 Z= 0.129 Angle : 0.638 15.747 7900 Z= 0.308 Chirality : 0.049 0.141 1005 Planarity : 0.003 0.028 1015 Dihedral : 4.435 28.160 835 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.94 % Favored : 89.43 % Rotamer: Outliers : 2.70 % Allowed : 20.00 % 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: -1.92 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.87 (0.45), residues: 135 loop : -1.95 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 182 HIS 0.002 0.001 HIS D 63 PHE 0.005 0.001 PHE C 60 TYR 0.013 0.001 TYR B 172 ARG 0.001 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.02583 ( 126) hydrogen bonds : angle 3.96932 ( 264) SS BOND : bond 0.00511 ( 5) SS BOND : angle 1.34486 ( 10) covalent geometry : bond 0.00306 ( 5740) covalent geometry : angle 0.63632 ( 7890) *********************** 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 88 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.644 Fit side-chains REVERT: B 84 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8502 (tt0) REVERT: C 59 ASP cc_start: 0.8349 (t0) cc_final: 0.8110 (t0) REVERT: C 96 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7924 (p0) outliers start: 17 outliers final: 13 residues processed: 86 average time/residue: 0.1115 time to fit residues: 14.5361 Evaluate side-chains 82 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 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 D residue 36 VAL 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: 2.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.0670 chunk 51 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.087643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.074850 restraints weight = 11692.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.077545 restraints weight = 6310.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.079405 restraints weight = 4119.855| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5745 Z= 0.172 Angle : 0.694 15.918 7900 Z= 0.335 Chirality : 0.050 0.143 1005 Planarity : 0.004 0.028 1015 Dihedral : 4.590 29.152 835 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.72 % Favored : 87.64 % Rotamer: Outliers : 2.70 % Allowed : 20.32 % 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: -1.99 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.78 (0.45), residues: 135 loop : -1.99 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 182 HIS 0.003 0.001 HIS D 63 PHE 0.006 0.001 PHE C 60 TYR 0.011 0.001 TYR B 172 ARG 0.002 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 126) hydrogen bonds : angle 3.99709 ( 264) SS BOND : bond 0.01064 ( 5) SS BOND : angle 3.08903 ( 10) covalent geometry : bond 0.00418 ( 5740) covalent geometry : angle 0.68564 ( 7890) *********************** 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 86 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.598 Fit side-chains REVERT: B 84 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8569 (tt0) REVERT: C 59 ASP cc_start: 0.8333 (t0) cc_final: 0.8098 (t0) REVERT: C 96 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7980 (p0) outliers start: 17 outliers final: 15 residues processed: 84 average time/residue: 0.1118 time to fit residues: 14.2424 Evaluate side-chains 83 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 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 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 D residue 36 VAL Chi-restraints excluded: chain D residue 41 CYS 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 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: 0.5980 chunk 71 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** 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 = 0.087855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.075042 restraints weight = 11709.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.077737 restraints weight = 6340.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.079598 restraints weight = 4150.994| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5745 Z= 0.128 Angle : 0.660 15.676 7900 Z= 0.313 Chirality : 0.049 0.139 1005 Planarity : 0.003 0.027 1015 Dihedral : 4.286 26.380 835 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.81 % Favored : 89.55 % Rotamer: Outliers : 2.70 % Allowed : 20.32 % 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: -1.93 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.86 (0.45), residues: 135 loop : -1.96 (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 E 100 PHE 0.005 0.001 PHE C 60 TYR 0.009 0.001 TYR B 172 ARG 0.001 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.02473 ( 126) hydrogen bonds : angle 3.90866 ( 264) SS BOND : bond 0.00962 ( 5) SS BOND : angle 2.41072 ( 10) covalent geometry : bond 0.00307 ( 5740) covalent geometry : angle 0.65453 ( 7890) *********************** 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 87 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.592 Fit side-chains REVERT: B 84 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8553 (tt0) REVERT: C 96 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7914 (p0) outliers start: 17 outliers final: 15 residues processed: 85 average time/residue: 0.1051 time to fit residues: 13.5413 Evaluate side-chains 83 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 75 VAL 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 D residue 36 VAL Chi-restraints excluded: chain D residue 41 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 25 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.090145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.078012 restraints weight = 11698.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.080549 restraints weight = 6560.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.082289 restraints weight = 4358.276| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5745 Z= 0.139 Angle : 0.668 15.539 7900 Z= 0.319 Chirality : 0.049 0.140 1005 Planarity : 0.003 0.027 1015 Dihedral : 4.317 26.135 835 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.70 % Favored : 88.66 % Rotamer: Outliers : 2.86 % Allowed : 20.32 % Favored : 76.83 % 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: -1.97 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.85 (0.45), residues: 135 loop : -2.00 (0.23), 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 0.004 0.001 PHE C 60 TYR 0.009 0.001 TYR E 172 ARG 0.002 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.02570 ( 126) hydrogen bonds : angle 3.93409 ( 264) SS BOND : bond 0.00808 ( 5) SS BOND : angle 2.21690 ( 10) covalent geometry : bond 0.00334 ( 5740) covalent geometry : angle 0.66410 ( 7890) ********************** 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 85 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.601 Fit side-chains REVERT: C 96 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7945 (p0) outliers start: 18 outliers final: 16 residues processed: 83 average time/residue: 0.1085 time to fit residues: 13.7597 Evaluate side-chains 82 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain B residue 75 VAL 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 D residue 36 VAL Chi-restraints excluded: chain D residue 41 CYS 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 150 ASN 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: 0.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 0.0050 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- 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 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 = 0.3181 r_free = 0.3181 target = 0.089669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.077519 restraints weight = 11775.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080056 restraints weight = 6565.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.081792 restraints weight = 4359.035| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5745 Z= 0.144 Angle : 1.077 59.180 7900 Z= 0.598 Chirality : 0.049 0.166 1005 Planarity : 0.003 0.027 1015 Dihedral : 4.334 26.093 835 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.70 % Favored : 88.66 % Rotamer: Outliers : 3.33 % Allowed : 19.68 % 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: -1.98 (0.29), residues: 785 helix: None (None), residues: 0 sheet: 0.86 (0.45), residues: 135 loop : -2.00 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 182 HIS 0.002 0.001 HIS D 63 PHE 0.004 0.001 PHE C 60 TYR 0.008 0.001 TYR B 172 ARG 0.001 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.02534 ( 126) hydrogen bonds : angle 3.93289 ( 264) SS BOND : bond 0.00793 ( 5) SS BOND : angle 2.17065 ( 10) covalent geometry : bond 0.00325 ( 5740) covalent geometry : angle 1.07509 ( 7890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2105.70 seconds wall clock time: 37 minutes 54.48 seconds (2274.48 seconds total)