Starting phenix.real_space_refine on Sun Mar 10 19:17:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/03_2024/6r4r_4727.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/03_2024/6r4r_4727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/03_2024/6r4r_4727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/03_2024/6r4r_4727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/03_2024/6r4r_4727.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/03_2024/6r4r_4727.pdb" } resolution = 3.4 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= 0.011 sd= 0.467 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 7 5.16 5 C 2723 2.51 5 N 686 2.21 5 O 896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4312 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "B" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "C" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "E" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "G" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Time building chain proxies: 2.71, per 1000 atoms: 0.63 Number of scatterers: 4312 At special positions: 0 Unit cell: (90.695, 115.005, 44.88, 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 7 16.00 O 896 8.00 N 686 7.00 C 2723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.69 Conformation dependent library (CDL) restraints added in 772.0 milliseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.618A pdb=" N LYS A 16 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLU C 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG A 18 " --> pdb=" O GLU C 19 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS C 16 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU E 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG C 18 " --> pdb=" O GLU E 19 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS E 16 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU G 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG E 18 " --> pdb=" O GLU G 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 25 removed outlier: 6.538A pdb=" N ASP A 23 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 23 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP E 23 " --> pdb=" O LEU G 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 37 through 41 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 56 removed outlier: 6.149A pdb=" N GLU A 51 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLY C 54 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 53 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU C 56 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP A 55 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU C 51 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY E 54 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 53 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU E 56 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N TRP C 55 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU E 51 " --> pdb=" O GLU G 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY G 54 " --> pdb=" O GLU E 51 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE E 53 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU G 56 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP E 55 " --> pdb=" O LEU G 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 61 through 68 Processing sheet with id=AA8, first strand: chain 'A' and resid 71 through 76 Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.617A pdb=" N LYS B 16 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU D 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 18 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS D 16 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG D 18 " --> pdb=" O GLU F 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 23 through 25 removed outlier: 6.538A pdb=" N ASP B 23 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP D 23 " --> pdb=" O LEU F 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 29 through 34 Processing sheet with id=AB4, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.151A pdb=" N GLU B 51 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY D 54 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 53 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU D 56 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N TRP B 55 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU D 51 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY F 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 53 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU F 56 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP D 55 " --> pdb=" O LEU F 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 61 through 68 Processing sheet with id=AB7, first strand: chain 'B' and resid 71 through 76 110 hydrogen bonds defined for protein. 330 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: 1.01 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1415 1.34 - 1.45: 707 1.45 - 1.57: 2267 1.57 - 1.69: 0 1.69 - 1.80: 14 Bond restraints: 4403 Sorted by residual: bond pdb=" CG LEU C 30 " pdb=" CD1 LEU C 30 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.98e+00 bond pdb=" CG LEU G 30 " pdb=" CD1 LEU G 30 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.94e+00 bond pdb=" CG LEU E 30 " pdb=" CD1 LEU E 30 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CG LEU A 30 " pdb=" CD1 LEU A 30 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CG LEU D 30 " pdb=" CD1 LEU D 30 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.89e+00 ... (remaining 4398 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.91: 99 106.91 - 113.64: 2147 113.64 - 120.36: 1875 120.36 - 127.09: 1766 127.09 - 133.82: 56 Bond angle restraints: 5943 Sorted by residual: angle pdb=" C GLU C 20 " pdb=" N ASP C 21 " pdb=" CA ASP C 21 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C GLU F 20 " pdb=" N ASP F 21 " pdb=" CA ASP F 21 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C GLU E 20 " pdb=" N ASP E 21 " pdb=" CA ASP E 21 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLU G 20 " pdb=" N ASP G 21 " pdb=" CA ASP G 21 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLU D 20 " pdb=" N ASP D 21 " pdb=" CA ASP D 21 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 ... (remaining 5938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.72: 1867 7.72 - 15.43: 499 15.43 - 23.15: 119 23.15 - 30.87: 35 30.87 - 38.59: 35 Dihedral angle restraints: 2555 sinusoidal: 1036 harmonic: 1519 Sorted by residual: dihedral pdb=" CA GLY E 5 " pdb=" C GLY E 5 " pdb=" N TYR E 6 " pdb=" CA TYR E 6 " ideal model delta harmonic sigma weight residual -180.00 -159.56 -20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLY G 5 " pdb=" C GLY G 5 " pdb=" N TYR G 6 " pdb=" CA TYR G 6 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLY C 5 " pdb=" C GLY C 5 " pdb=" N TYR C 6 " pdb=" CA TYR C 6 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 2552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 405 0.069 - 0.137: 162 0.137 - 0.206: 21 0.206 - 0.275: 0 0.275 - 0.344: 7 Chirality restraints: 595 Sorted by residual: chirality pdb=" CA ASP F 21 " pdb=" N ASP F 21 " pdb=" C ASP F 21 " pdb=" CB ASP F 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ASP D 21 " pdb=" N ASP D 21 " pdb=" C ASP D 21 " pdb=" CB ASP D 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASP A 21 " pdb=" N ASP A 21 " pdb=" C ASP A 21 " pdb=" CB ASP A 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 592 not shown) Planarity restraints: 791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 48 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C ALA C 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA C 48 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS C 49 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 48 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C ALA E 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA E 48 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS E 49 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 48 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C ALA G 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA G 48 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS G 49 " -0.018 2.00e-02 2.50e+03 ... (remaining 788 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1211 2.83 - 3.34: 3397 3.34 - 3.86: 7837 3.86 - 4.38: 8251 4.38 - 4.90: 15637 Nonbonded interactions: 36333 Sorted by model distance: nonbonded pdb=" OE2 GLU A 47 " pdb=" NZ LYS A 49 " model vdw 2.308 2.520 nonbonded pdb=" OE2 GLU B 47 " pdb=" NZ LYS B 49 " model vdw 2.309 2.520 nonbonded pdb=" OE2 GLU F 47 " pdb=" NZ LYS F 49 " model vdw 2.310 2.520 nonbonded pdb=" OE2 GLU E 47 " pdb=" NZ LYS E 49 " model vdw 2.310 2.520 nonbonded pdb=" OE2 GLU C 47 " pdb=" NZ LYS C 49 " model vdw 2.310 2.520 ... (remaining 36328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.490 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: 2.470 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 16.000 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 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 : 0.008 0.057 4403 Z= 0.504 Angle : 1.430 15.584 5943 Z= 0.726 Chirality : 0.075 0.344 595 Planarity : 0.008 0.054 791 Dihedral : 10.872 38.585 1617 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -5.16 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 55 HIS 0.018 0.011 HIS A 25 PHE 0.008 0.003 PHE B 69 TYR 0.017 0.004 TYR B 8 ARG 0.003 0.001 ARG G 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.476 Fit side-chains REVERT: A 66 ARG cc_start: 0.7176 (ttm110) cc_final: 0.5303 (tpt170) REVERT: B 66 ARG cc_start: 0.7045 (ttm110) cc_final: 0.5719 (tpt170) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1599 time to fit residues: 39.2663 Evaluate side-chains 116 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS E 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4403 Z= 0.205 Angle : 0.741 10.285 5943 Z= 0.361 Chirality : 0.046 0.189 595 Planarity : 0.005 0.037 791 Dihedral : 5.937 16.474 602 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.95 % Allowed : 11.56 % Favored : 85.49 % 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: -4.92 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 55 HIS 0.005 0.001 HIS F 25 PHE 0.013 0.002 PHE D 69 TYR 0.022 0.002 TYR E 59 ARG 0.014 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7058 (ttm110) cc_final: 0.5559 (tpt170) REVERT: B 69 PHE cc_start: 0.7664 (m-80) cc_final: 0.5192 (p90) REVERT: E 55 TRP cc_start: 0.7213 (t-100) cc_final: 0.6920 (t-100) outliers start: 13 outliers final: 6 residues processed: 136 average time/residue: 0.1484 time to fit residues: 25.5581 Evaluate side-chains 111 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain G residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 12 optimal weight: 0.0000 chunk 44 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 overall best weight: 3.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4403 Z= 0.195 Angle : 0.651 10.487 5943 Z= 0.326 Chirality : 0.044 0.161 595 Planarity : 0.004 0.032 791 Dihedral : 5.441 16.960 602 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 3.85 % Allowed : 14.74 % Favored : 81.41 % 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: -4.79 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 55 HIS 0.001 0.001 HIS B 25 PHE 0.020 0.002 PHE A 69 TYR 0.019 0.002 TYR D 8 ARG 0.009 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.574 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 127 average time/residue: 0.1524 time to fit residues: 24.4941 Evaluate side-chains 110 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4403 Z= 0.159 Angle : 0.593 9.552 5943 Z= 0.291 Chirality : 0.042 0.136 595 Planarity : 0.003 0.028 791 Dihedral : 4.976 16.013 602 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 4.76 % Allowed : 16.78 % Favored : 78.46 % 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: -4.61 (0.26), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.20), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 55 HIS 0.001 0.000 HIS E 25 PHE 0.021 0.002 PHE A 69 TYR 0.019 0.001 TYR E 8 ARG 0.006 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.530 Fit side-chains REVERT: D 44 ASP cc_start: 0.5767 (m-30) cc_final: 0.5511 (m-30) REVERT: F 66 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.6122 (ttp-170) outliers start: 21 outliers final: 10 residues processed: 125 average time/residue: 0.1377 time to fit residues: 22.2481 Evaluate side-chains 115 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 30.0000 chunk 19 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 40.0000 chunk 42 optimal weight: 30.0000 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 overall best weight: 8.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4403 Z= 0.350 Angle : 0.750 10.063 5943 Z= 0.384 Chirality : 0.048 0.148 595 Planarity : 0.005 0.034 791 Dihedral : 5.707 17.407 602 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 7.71 % Allowed : 15.87 % Favored : 76.42 % 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: -4.62 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 55 HIS 0.001 0.000 HIS G 25 PHE 0.021 0.002 PHE A 69 TYR 0.020 0.003 TYR E 8 ARG 0.008 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7978 (pt) outliers start: 34 outliers final: 25 residues processed: 121 average time/residue: 0.1232 time to fit residues: 19.7927 Evaluate side-chains 117 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4403 Z= 0.289 Angle : 0.685 10.522 5943 Z= 0.347 Chirality : 0.046 0.140 595 Planarity : 0.004 0.040 791 Dihedral : 5.581 20.806 602 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 7.71 % Allowed : 16.78 % Favored : 75.51 % 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: -4.65 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 55 HIS 0.002 0.001 HIS F 25 PHE 0.019 0.002 PHE A 69 TYR 0.020 0.002 TYR D 8 ARG 0.008 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 97 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.5547 (OUTLIER) cc_final: 0.5269 (pt) REVERT: B 69 PHE cc_start: 0.6782 (m-10) cc_final: 0.4755 (p90) REVERT: E 55 TRP cc_start: 0.7225 (t-100) cc_final: 0.7014 (t60) REVERT: E 69 PHE cc_start: 0.8081 (m-80) cc_final: 0.7794 (m-80) REVERT: G 69 PHE cc_start: 0.6841 (m-80) cc_final: 0.5280 (m-80) outliers start: 34 outliers final: 20 residues processed: 118 average time/residue: 0.1515 time to fit residues: 22.6690 Evaluate side-chains 111 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4403 Z= 0.298 Angle : 0.694 7.817 5943 Z= 0.353 Chirality : 0.046 0.143 595 Planarity : 0.004 0.042 791 Dihedral : 5.574 19.338 602 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 8.84 % Allowed : 15.65 % Favored : 75.51 % 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: -4.69 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 55 HIS 0.002 0.001 HIS B 25 PHE 0.018 0.002 PHE A 69 TYR 0.021 0.002 TYR D 8 ARG 0.007 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 96 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.5534 (OUTLIER) cc_final: 0.5249 (pt) REVERT: E 55 TRP cc_start: 0.7124 (t-100) cc_final: 0.6922 (t60) REVERT: F 69 PHE cc_start: 0.6537 (m-80) cc_final: 0.5512 (m-80) REVERT: G 69 PHE cc_start: 0.6399 (m-80) cc_final: 0.5234 (m-80) outliers start: 39 outliers final: 24 residues processed: 120 average time/residue: 0.1413 time to fit residues: 21.7522 Evaluate side-chains 116 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 chunk 37 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4403 Z= 0.212 Angle : 0.635 8.692 5943 Z= 0.318 Chirality : 0.044 0.141 595 Planarity : 0.004 0.039 791 Dihedral : 5.294 21.800 602 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 7.48 % Allowed : 16.78 % Favored : 75.74 % 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: -4.70 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 55 HIS 0.002 0.001 HIS B 25 PHE 0.018 0.002 PHE D 69 TYR 0.020 0.002 TYR D 8 ARG 0.004 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 102 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.5481 (OUTLIER) cc_final: 0.5221 (pt) REVERT: B 30 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6975 (tt) REVERT: D 47 GLU cc_start: 0.5043 (mm-30) cc_final: 0.4815 (mm-30) REVERT: E 69 PHE cc_start: 0.7836 (m-80) cc_final: 0.7311 (m-80) REVERT: F 69 PHE cc_start: 0.6179 (m-80) cc_final: 0.5496 (m-80) REVERT: G 69 PHE cc_start: 0.5965 (m-80) cc_final: 0.5398 (m-80) outliers start: 33 outliers final: 26 residues processed: 121 average time/residue: 0.1398 time to fit residues: 21.8297 Evaluate side-chains 125 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4403 Z= 0.323 Angle : 0.718 8.716 5943 Z= 0.366 Chirality : 0.047 0.142 595 Planarity : 0.005 0.041 791 Dihedral : 5.610 21.178 602 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 7.48 % Allowed : 17.23 % Favored : 75.28 % 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: -4.74 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 55 HIS 0.003 0.001 HIS B 25 PHE 0.018 0.003 PHE A 69 TYR 0.028 0.003 TYR C 59 ARG 0.007 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.5617 (OUTLIER) cc_final: 0.5355 (pt) REVERT: B 46 GLN cc_start: 0.4588 (OUTLIER) cc_final: 0.4058 (pp30) REVERT: D 66 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7999 (ttp-110) REVERT: E 69 PHE cc_start: 0.7995 (m-80) cc_final: 0.7481 (m-80) REVERT: G 69 PHE cc_start: 0.6150 (m-80) cc_final: 0.5359 (m-80) outliers start: 33 outliers final: 21 residues processed: 115 average time/residue: 0.1358 time to fit residues: 20.4468 Evaluate side-chains 117 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.6884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4403 Z= 0.262 Angle : 0.683 8.926 5943 Z= 0.341 Chirality : 0.046 0.156 595 Planarity : 0.004 0.039 791 Dihedral : 5.472 21.244 602 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 6.58 % Allowed : 17.46 % Favored : 75.96 % 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: -4.75 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 55 HIS 0.002 0.001 HIS B 25 PHE 0.026 0.003 PHE B 69 TYR 0.025 0.002 TYR C 59 ARG 0.005 0.001 ARG C 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: A 29 ILE cc_start: 0.5577 (OUTLIER) cc_final: 0.5307 (pt) REVERT: B 46 GLN cc_start: 0.4813 (OUTLIER) cc_final: 0.4196 (pp30) REVERT: D 47 GLU cc_start: 0.4948 (mm-30) cc_final: 0.4638 (mm-30) REVERT: E 47 GLU cc_start: 0.4728 (tp30) cc_final: 0.4482 (tp30) REVERT: E 69 PHE cc_start: 0.7874 (m-80) cc_final: 0.7494 (m-80) REVERT: F 69 PHE cc_start: 0.6319 (m-80) cc_final: 0.5534 (m-80) REVERT: G 69 PHE cc_start: 0.5780 (m-80) cc_final: 0.5434 (m-80) outliers start: 29 outliers final: 22 residues processed: 113 average time/residue: 0.1504 time to fit residues: 21.7099 Evaluate side-chains 119 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 overall best weight: 7.9994 ------------------------------------------------------------------------------- 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 = 0.4857 r_free = 0.4857 target = 0.197848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.177052 restraints weight = 8084.850| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 2.85 r_work: 0.4647 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4403 Z= 0.331 Angle : 0.735 8.848 5943 Z= 0.371 Chirality : 0.047 0.155 595 Planarity : 0.005 0.039 791 Dihedral : 5.688 21.851 602 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 6.35 % Allowed : 19.05 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 55 HIS 0.003 0.001 HIS B 25 PHE 0.018 0.003 PHE C 69 TYR 0.024 0.003 TYR C 59 ARG 0.006 0.001 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1192.23 seconds wall clock time: 22 minutes 17.16 seconds (1337.16 seconds total)