Starting phenix.real_space_refine on Mon Jan 13 21:36:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eme_19818/01_2025/9eme_19818.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eme_19818/01_2025/9eme_19818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eme_19818/01_2025/9eme_19818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eme_19818/01_2025/9eme_19818.map" model { file = "/net/cci-nas-00/data/ceres_data/9eme_19818/01_2025/9eme_19818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eme_19818/01_2025/9eme_19818.cif" } resolution = 2.92 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 12 5.16 5 C 2562 2.51 5 N 714 2.21 5 O 852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4140 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 690 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.40, per 1000 atoms: 0.58 Number of scatterers: 4140 At special positions: 0 Unit cell: (79.04, 92.56, 52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 852 8.00 N 714 7.00 C 2562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 484.5 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23 removed outlier: 6.582A pdb=" N GLN A 16 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG B 19 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 18 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR B 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 20 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN B 23 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS A 22 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN B 16 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG C 19 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 18 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR C 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE B 20 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN C 23 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS B 22 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN C 16 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG D 19 " --> pdb=" O GLN C 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 18 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR D 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE C 20 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN D 23 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS C 22 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN D 16 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG E 19 " --> pdb=" O GLN D 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL D 18 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR E 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 20 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN E 23 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS D 22 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN E 16 " --> pdb=" O THR F 17 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ARG F 19 " --> pdb=" O GLN E 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL E 18 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR F 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE E 20 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN F 23 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS E 22 " --> pdb=" O GLN F 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.844A pdb=" N LEU A 45 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 45 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 45 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU D 45 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 45 " --> pdb=" O VAL F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 78 removed outlier: 6.757A pdb=" N ALA B 77 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN A 78 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 77 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN B 78 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA D 77 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN C 78 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA E 77 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN D 78 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA F 77 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN E 78 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 81 through 83 removed outlier: 8.450A pdb=" N ASP A 81 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP B 81 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP C 81 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP D 81 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP E 81 " --> pdb=" O GLU F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 103 through 106 80 hydrogen bonds defined for protein. 240 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: 1.00 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 690 1.30 - 1.43: 1224 1.43 - 1.55: 2286 1.55 - 1.68: 0 1.68 - 1.81: 12 Bond restraints: 4212 Sorted by residual: bond pdb=" C VAL A 46 " pdb=" O VAL A 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.47e+01 bond pdb=" C VAL F 46 " pdb=" O VAL F 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.46e+01 bond pdb=" C VAL E 46 " pdb=" O VAL E 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.46e+01 bond pdb=" C VAL D 46 " pdb=" O VAL D 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.45e+01 bond pdb=" C VAL B 46 " pdb=" O VAL B 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.45e+01 ... (remaining 4207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 3919 1.92 - 3.84: 1269 3.84 - 5.76: 458 5.76 - 7.68: 60 7.68 - 9.61: 6 Bond angle restraints: 5712 Sorted by residual: angle pdb=" N SER F 64 " pdb=" CA SER F 64 " pdb=" C SER F 64 " ideal model delta sigma weight residual 110.97 120.58 -9.61 1.09e+00 8.42e-01 7.77e+01 angle pdb=" N SER C 64 " pdb=" CA SER C 64 " pdb=" C SER C 64 " ideal model delta sigma weight residual 110.97 120.56 -9.59 1.09e+00 8.42e-01 7.75e+01 angle pdb=" N SER D 64 " pdb=" CA SER D 64 " pdb=" C SER D 64 " ideal model delta sigma weight residual 110.97 120.54 -9.57 1.09e+00 8.42e-01 7.71e+01 angle pdb=" N SER E 64 " pdb=" CA SER E 64 " pdb=" C SER E 64 " ideal model delta sigma weight residual 110.97 120.53 -9.56 1.09e+00 8.42e-01 7.70e+01 angle pdb=" N SER A 64 " pdb=" CA SER A 64 " pdb=" C SER A 64 " ideal model delta sigma weight residual 110.97 120.53 -9.56 1.09e+00 8.42e-01 7.69e+01 ... (remaining 5707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 2145 14.03 - 28.06: 156 28.06 - 42.09: 84 42.09 - 56.12: 24 56.12 - 70.15: 6 Dihedral angle restraints: 2415 sinusoidal: 849 harmonic: 1566 Sorted by residual: dihedral pdb=" C HIS E 95 " pdb=" N HIS E 95 " pdb=" CA HIS E 95 " pdb=" CB HIS E 95 " ideal model delta harmonic sigma weight residual -122.60 -131.87 9.27 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" C HIS F 95 " pdb=" N HIS F 95 " pdb=" CA HIS F 95 " pdb=" CB HIS F 95 " ideal model delta harmonic sigma weight residual -122.60 -131.86 9.26 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C HIS C 95 " pdb=" N HIS C 95 " pdb=" CA HIS C 95 " pdb=" CB HIS C 95 " ideal model delta harmonic sigma weight residual -122.60 -131.86 9.26 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 2412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 228 0.062 - 0.124: 186 0.124 - 0.186: 142 0.186 - 0.248: 62 0.248 - 0.310: 18 Chirality restraints: 636 Sorted by residual: chirality pdb=" CA HIS B 95 " pdb=" N HIS B 95 " pdb=" C HIS B 95 " pdb=" CB HIS B 95 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA HIS A 95 " pdb=" N HIS A 95 " pdb=" C HIS A 95 " pdb=" CB HIS A 95 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA HIS D 95 " pdb=" N HIS D 95 " pdb=" C HIS D 95 " pdb=" CB HIS D 95 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 633 not shown) Planarity restraints: 738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 100 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C GLY E 100 " -0.072 2.00e-02 2.50e+03 pdb=" O GLY E 100 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY E 101 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 100 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C GLY B 100 " -0.072 2.00e-02 2.50e+03 pdb=" O GLY B 100 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY B 101 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 100 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C GLY C 100 " -0.072 2.00e-02 2.50e+03 pdb=" O GLY C 100 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY C 101 " 0.025 2.00e-02 2.50e+03 ... (remaining 735 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 23 2.59 - 3.17: 3317 3.17 - 3.75: 6377 3.75 - 4.32: 8956 4.32 - 4.90: 17467 Nonbonded interactions: 36140 Sorted by model distance: nonbonded pdb=" SG CYS B 22 " pdb=" SG CYS B 87 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS C 22 " pdb=" SG CYS C 87 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS E 22 " pdb=" SG CYS E 87 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS D 22 " pdb=" SG CYS D 87 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS F 22 " pdb=" SG CYS F 87 " model vdw 2.019 3.760 ... (remaining 36135 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.990 Find NCS groups from input model: 0.090 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 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 : 0.015 0.065 4212 Z= 0.991 Angle : 2.116 9.606 5712 Z= 1.591 Chirality : 0.121 0.310 636 Planarity : 0.012 0.042 738 Dihedral : 14.206 70.153 1428 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % 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: -4.40 (0.21), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.16), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP C 34 HIS 0.007 0.003 HIS B 95 PHE 0.006 0.002 PHE C 61 TYR 0.014 0.002 TYR B 30 ARG 0.007 0.002 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.451 Fit side-chains REVERT: A 23 GLN cc_start: 0.7914 (tt0) cc_final: 0.6979 (tm-30) REVERT: A 89 SER cc_start: 0.6068 (t) cc_final: 0.5827 (t) REVERT: B 23 GLN cc_start: 0.6604 (tt0) cc_final: 0.5670 (tm-30) REVERT: C 19 ARG cc_start: 0.5982 (ttm170) cc_final: 0.5702 (ttm170) REVERT: C 23 GLN cc_start: 0.6797 (tt0) cc_final: 0.5708 (tm-30) REVERT: C 27 LEU cc_start: 0.6638 (tt) cc_final: 0.6275 (mp) REVERT: D 23 GLN cc_start: 0.7023 (tt0) cc_final: 0.5726 (tm-30) REVERT: D 33 SER cc_start: 0.7831 (p) cc_final: 0.7617 (p) REVERT: D 38 LYS cc_start: 0.7392 (mttt) cc_final: 0.7167 (mtpp) REVERT: D 78 GLN cc_start: 0.7055 (mt0) cc_final: 0.6721 (mt0) REVERT: F 23 GLN cc_start: 0.6897 (tt0) cc_final: 0.6431 (tm-30) REVERT: F 78 GLN cc_start: 0.7283 (mt0) cc_final: 0.6979 (mt0) REVERT: F 80 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6218 (tt0) REVERT: F 90 ARG cc_start: 0.6815 (ttt180) cc_final: 0.6035 (tpm170) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 1.0532 time to fit residues: 131.2919 Evaluate side-chains 61 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 68 ASN A 78 GLN B 52 ASN B 68 ASN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 78 GLN D 68 ASN E 16 GLN E 68 ASN E 78 GLN F 65 ASN F 68 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.121254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.110214 restraints weight = 5507.523| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.01 r_work: 0.3800 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4212 Z= 0.175 Angle : 0.568 6.836 5712 Z= 0.320 Chirality : 0.045 0.121 636 Planarity : 0.002 0.032 738 Dihedral : 5.041 17.926 600 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.93 % Allowed : 16.89 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 34 HIS 0.002 0.001 HIS E 95 PHE 0.004 0.001 PHE E 61 TYR 0.011 0.002 TYR A 31 ARG 0.003 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.444 Fit side-chains REVERT: A 38 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8530 (mttt) REVERT: E 90 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7555 (ttp80) REVERT: F 23 GLN cc_start: 0.7898 (tt0) cc_final: 0.7521 (tm-30) REVERT: F 80 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7876 (tt0) REVERT: F 90 ARG cc_start: 0.8063 (ttt180) cc_final: 0.6959 (tpm170) outliers start: 13 outliers final: 2 residues processed: 60 average time/residue: 1.1694 time to fit residues: 72.9567 Evaluate side-chains 47 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain F residue 49 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 5 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 42 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN B 78 GLN D 68 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN F 78 GLN ** F 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.124802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.113531 restraints weight = 5418.547| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.04 r_work: 0.3876 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4212 Z= 0.135 Angle : 0.499 5.965 5712 Z= 0.281 Chirality : 0.044 0.115 636 Planarity : 0.002 0.025 738 Dihedral : 4.585 17.250 600 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.58 % Allowed : 18.02 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 34 HIS 0.001 0.001 HIS A 95 PHE 0.003 0.001 PHE C 61 TYR 0.009 0.001 TYR C 35 ARG 0.002 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8502 (mttt) REVERT: D 90 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7918 (ttp80) REVERT: E 90 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7270 (ttm-80) REVERT: F 80 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7934 (tt0) REVERT: F 90 ARG cc_start: 0.8049 (ttt180) cc_final: 0.6867 (tpm170) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 1.2423 time to fit residues: 67.1537 Evaluate side-chains 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 38 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN D 68 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN F 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.117433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.106066 restraints weight = 5784.936| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.08 r_work: 0.3775 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4212 Z= 0.269 Angle : 0.552 5.444 5712 Z= 0.310 Chirality : 0.045 0.165 636 Planarity : 0.002 0.019 738 Dihedral : 5.078 19.389 600 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.58 % Allowed : 16.67 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 34 HIS 0.005 0.002 HIS D 95 PHE 0.004 0.001 PHE A 99 TYR 0.016 0.002 TYR A 30 ARG 0.002 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8486 (mttt) REVERT: A 90 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7524 (ttm170) REVERT: C 19 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7618 (ttm170) REVERT: F 90 ARG cc_start: 0.7811 (ttt180) cc_final: 0.6490 (tpm170) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 1.3354 time to fit residues: 56.8829 Evaluate side-chains 42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 19 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 5 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 ASN D 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.115121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.103895 restraints weight = 6040.319| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.10 r_work: 0.3756 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4212 Z= 0.306 Angle : 0.565 5.271 5712 Z= 0.315 Chirality : 0.045 0.146 636 Planarity : 0.002 0.026 738 Dihedral : 5.151 18.272 600 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.70 % Allowed : 15.99 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 34 HIS 0.005 0.002 HIS C 95 PHE 0.006 0.001 PHE B 99 TYR 0.016 0.002 TYR A 30 ARG 0.005 0.001 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8478 (mttt) REVERT: C 19 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7588 (ttm170) REVERT: C 82 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7707 (mt-10) REVERT: E 90 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7296 (ptm160) REVERT: F 90 ARG cc_start: 0.7831 (ttt180) cc_final: 0.6657 (ttm170) outliers start: 12 outliers final: 3 residues processed: 48 average time/residue: 1.4537 time to fit residues: 72.1503 Evaluate side-chains 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 19 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.120623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.109040 restraints weight = 5640.456| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.09 r_work: 0.3807 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4212 Z= 0.180 Angle : 0.509 6.243 5712 Z= 0.279 Chirality : 0.044 0.122 636 Planarity : 0.002 0.027 738 Dihedral : 4.714 17.598 600 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.35 % Allowed : 16.89 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 34 HIS 0.003 0.001 HIS D 95 PHE 0.003 0.001 PHE A 61 TYR 0.011 0.001 TYR A 30 ARG 0.004 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8430 (mttt) REVERT: C 19 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7560 (ttm170) REVERT: D 38 LYS cc_start: 0.8704 (mttp) cc_final: 0.8338 (mptt) REVERT: E 90 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7280 (ptm160) REVERT: F 90 ARG cc_start: 0.7832 (ttt180) cc_final: 0.6618 (ttm170) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 1.1840 time to fit residues: 53.0862 Evaluate side-chains 42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain D residue 68 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.113231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.102066 restraints weight = 5986.625| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.07 r_work: 0.3715 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 4212 Z= 0.418 Angle : 0.627 6.237 5712 Z= 0.345 Chirality : 0.047 0.177 636 Planarity : 0.003 0.031 738 Dihedral : 5.550 21.953 600 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.13 % Allowed : 20.72 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 34 HIS 0.008 0.003 HIS D 95 PHE 0.008 0.002 PHE B 99 TYR 0.020 0.003 TYR A 30 ARG 0.003 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.493 Fit side-chains REVERT: A 38 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8488 (mttt) REVERT: A 90 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7538 (ttm110) REVERT: C 19 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7666 (ttm170) REVERT: C 82 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7911 (mm-30) REVERT: E 90 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7342 (ptm160) REVERT: F 90 ARG cc_start: 0.7938 (ttt180) cc_final: 0.6582 (ttm170) outliers start: 5 outliers final: 2 residues processed: 39 average time/residue: 1.3867 time to fit residues: 56.0692 Evaluate side-chains 40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 19 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.119035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.107402 restraints weight = 5651.230| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.09 r_work: 0.3785 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4212 Z= 0.209 Angle : 0.533 7.126 5712 Z= 0.289 Chirality : 0.044 0.132 636 Planarity : 0.002 0.021 738 Dihedral : 4.880 19.192 600 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.90 % Allowed : 21.40 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 34 HIS 0.003 0.001 HIS A 95 PHE 0.004 0.001 PHE E 61 TYR 0.011 0.001 TYR A 30 ARG 0.004 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.430 Fit side-chains REVERT: C 19 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7644 (ttm170) REVERT: D 38 LYS cc_start: 0.8753 (mttp) cc_final: 0.8341 (mptt) REVERT: E 90 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7293 (ptm160) REVERT: F 90 ARG cc_start: 0.7955 (ttt180) cc_final: 0.6519 (ttm170) outliers start: 4 outliers final: 1 residues processed: 38 average time/residue: 1.2914 time to fit residues: 51.0166 Evaluate side-chains 37 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 19 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.115904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.104470 restraints weight = 5850.110| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.08 r_work: 0.3749 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4212 Z= 0.297 Angle : 0.571 6.962 5712 Z= 0.310 Chirality : 0.045 0.145 636 Planarity : 0.003 0.043 738 Dihedral : 5.174 19.966 600 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.90 % Allowed : 22.30 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 34 HIS 0.006 0.002 HIS D 95 PHE 0.005 0.001 PHE B 99 TYR 0.015 0.002 TYR A 30 ARG 0.004 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7687 (ttm170) REVERT: D 38 LYS cc_start: 0.8810 (mttp) cc_final: 0.8370 (mptt) REVERT: E 90 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7307 (ptm160) REVERT: F 90 ARG cc_start: 0.7962 (ttt180) cc_final: 0.6509 (ttm170) outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 1.3145 time to fit residues: 49.2639 Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain D residue 68 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.121247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.109308 restraints weight = 5643.610| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.13 r_work: 0.3819 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4212 Z= 0.170 Angle : 0.515 7.230 5712 Z= 0.277 Chirality : 0.044 0.120 636 Planarity : 0.002 0.030 738 Dihedral : 4.671 17.284 600 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.90 % Allowed : 22.30 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 34 HIS 0.002 0.001 HIS A 95 PHE 0.004 0.001 PHE E 61 TYR 0.010 0.001 TYR A 35 ARG 0.004 0.000 ARG C 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7648 (ttm170) REVERT: D 38 LYS cc_start: 0.8707 (mttp) cc_final: 0.8336 (mptt) REVERT: E 90 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7234 (ptm160) REVERT: F 90 ARG cc_start: 0.7964 (ttt180) cc_final: 0.6425 (ttm170) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 1.3779 time to fit residues: 52.9685 Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain D residue 68 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.120839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.108986 restraints weight = 5562.412| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.10 r_work: 0.3813 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4212 Z= 0.186 Angle : 0.527 7.264 5712 Z= 0.283 Chirality : 0.044 0.123 636 Planarity : 0.002 0.030 738 Dihedral : 4.701 17.121 600 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.90 % Allowed : 22.52 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 34 HIS 0.003 0.001 HIS A 95 PHE 0.003 0.001 PHE E 61 TYR 0.011 0.001 TYR B 31 ARG 0.004 0.001 ARG C 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2759.43 seconds wall clock time: 50 minutes 7.13 seconds (3007.13 seconds total)