Starting phenix.real_space_refine on Sun Mar 10 18:19:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/03_2024/7ozh_13124.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/03_2024/7ozh_13124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/03_2024/7ozh_13124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/03_2024/7ozh_13124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/03_2024/7ozh_13124.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozh_13124/03_2024/7ozh_13124.pdb" } resolution = 3.02 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= 1.002 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: 3 Type Number sf(0) Gaussians C 2410 2.51 5 N 680 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 3890 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "C" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "D" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "E" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "F" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "G" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "H" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "I" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "J" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 389 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N LYS A 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS A 45 " occ=0.50 residue: pdb=" N LYS B 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS B 45 " occ=0.50 residue: pdb=" N LYS C 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS C 45 " occ=0.50 residue: pdb=" N LYS D 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS D 45 " occ=0.50 residue: pdb=" N LYS E 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS E 45 " occ=0.50 residue: pdb=" N LYS F 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS F 45 " occ=0.50 residue: pdb=" N LYS G 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS G 45 " occ=0.50 residue: pdb=" N LYS H 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS H 45 " occ=0.50 residue: pdb=" N LYS I 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS I 45 " occ=0.50 residue: pdb=" N LYS J 45 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS J 45 " occ=0.50 Time building chain proxies: 2.34, per 1000 atoms: 0.60 Number of scatterers: 3890 At special positions: 0 Unit cell: (116.55, 76.65, 43.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 800 8.00 N 680 7.00 C 2410 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: 1.49 Conformation dependent library (CDL) restraints added in 878.1 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 6.247A pdb=" N GLY A 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY C 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY E 41 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY G 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.507A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL C 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL E 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL G 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.845A pdb=" N THR A 75 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA C 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR C 75 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA E 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR E 75 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA G 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR G 75 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA I 76 " --> pdb=" O THR G 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.404A pdb=" N ILE A 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE C 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE E 88 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE G 88 " --> pdb=" O ALA I 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 42 removed outlier: 6.246A pdb=" N GLY B 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY D 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY F 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY H 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.509A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL D 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL F 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL H 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 76 removed outlier: 6.846A pdb=" N THR B 75 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA D 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR D 75 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA F 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR F 75 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA H 76 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR H 75 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA J 76 " --> pdb=" O THR H 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.404A pdb=" N ILE B 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE D 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE F 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE H 88 " --> pdb=" O ALA J 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 56 hydrogen bonds defined for protein. 168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.28: 690 1.28 - 1.35: 630 1.35 - 1.43: 269 1.43 - 1.51: 1434 1.51 - 1.58: 877 Bond restraints: 3900 Sorted by residual: bond pdb=" CA LYS D 45 " pdb=" CB LYS D 45 " ideal model delta sigma weight residual 1.535 1.446 0.089 2.02e-02 2.45e+03 1.95e+01 bond pdb=" CA LYS H 45 " pdb=" CB LYS H 45 " ideal model delta sigma weight residual 1.535 1.446 0.089 2.02e-02 2.45e+03 1.94e+01 bond pdb=" CA LYS E 45 " pdb=" CB LYS E 45 " ideal model delta sigma weight residual 1.535 1.446 0.089 2.02e-02 2.45e+03 1.93e+01 bond pdb=" CA LYS J 45 " pdb=" CB LYS J 45 " ideal model delta sigma weight residual 1.535 1.446 0.089 2.02e-02 2.45e+03 1.93e+01 bond pdb=" CA LYS G 45 " pdb=" CB LYS G 45 " ideal model delta sigma weight residual 1.535 1.446 0.089 2.02e-02 2.45e+03 1.93e+01 ... (remaining 3895 not shown) Histogram of bond angle deviations from ideal: 104.20 - 109.50: 869 109.50 - 114.79: 1781 114.79 - 120.09: 873 120.09 - 125.39: 1757 125.39 - 130.69: 10 Bond angle restraints: 5290 Sorted by residual: angle pdb=" C VAL A 52 " pdb=" CA VAL A 52 " pdb=" CB VAL A 52 " ideal model delta sigma weight residual 111.19 105.91 5.28 1.39e+00 5.18e-01 1.44e+01 angle pdb=" C VAL F 52 " pdb=" CA VAL F 52 " pdb=" CB VAL F 52 " ideal model delta sigma weight residual 111.19 105.93 5.26 1.39e+00 5.18e-01 1.43e+01 angle pdb=" C VAL E 52 " pdb=" CA VAL E 52 " pdb=" CB VAL E 52 " ideal model delta sigma weight residual 111.19 105.94 5.25 1.39e+00 5.18e-01 1.43e+01 angle pdb=" C VAL H 52 " pdb=" CA VAL H 52 " pdb=" CB VAL H 52 " ideal model delta sigma weight residual 111.19 105.94 5.25 1.39e+00 5.18e-01 1.43e+01 angle pdb=" C VAL J 52 " pdb=" CA VAL J 52 " pdb=" CB VAL J 52 " ideal model delta sigma weight residual 111.19 105.94 5.25 1.39e+00 5.18e-01 1.43e+01 ... (remaining 5285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.25: 1741 6.25 - 12.49: 419 12.49 - 18.73: 60 18.73 - 24.98: 20 24.98 - 31.22: 10 Dihedral angle restraints: 2250 sinusoidal: 710 harmonic: 1540 Sorted by residual: dihedral pdb=" CA GLU F 61 " pdb=" C GLU F 61 " pdb=" N GLN F 62 " pdb=" CA GLN F 62 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLU G 61 " pdb=" C GLU G 61 " pdb=" N GLN G 62 " pdb=" CA GLN G 62 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLU H 61 " pdb=" C GLU H 61 " pdb=" N GLN H 62 " pdb=" CA GLN H 62 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 2247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 260 0.045 - 0.089: 241 0.089 - 0.134: 99 0.134 - 0.178: 71 0.178 - 0.222: 39 Chirality restraints: 710 Sorted by residual: chirality pdb=" CB VAL H 49 " pdb=" CA VAL H 49 " pdb=" CG1 VAL H 49 " pdb=" CG2 VAL H 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL C 49 " pdb=" CA VAL C 49 " pdb=" CG1 VAL C 49 " pdb=" CG2 VAL C 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL G 49 " pdb=" CA VAL G 49 " pdb=" CG1 VAL G 49 " pdb=" CG2 VAL G 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 707 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 81 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C THR B 81 " 0.048 2.00e-02 2.50e+03 pdb=" O THR B 81 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL B 82 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 81 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C THR C 81 " -0.048 2.00e-02 2.50e+03 pdb=" O THR C 81 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 82 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 81 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.73e+00 pdb=" C THR I 81 " -0.048 2.00e-02 2.50e+03 pdb=" O THR I 81 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL I 82 " 0.016 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 2504 3.02 - 3.49: 4006 3.49 - 3.96: 5893 3.96 - 4.43: 6914 4.43 - 4.90: 13870 Nonbonded interactions: 33187 Sorted by model distance: nonbonded pdb=" N VAL A 82 " pdb=" O THR C 81 " model vdw 2.546 2.520 nonbonded pdb=" N VAL C 82 " pdb=" O THR E 81 " model vdw 2.546 2.520 nonbonded pdb=" N VAL E 82 " pdb=" O THR G 81 " model vdw 2.547 2.520 nonbonded pdb=" N VAL B 82 " pdb=" O THR D 81 " model vdw 2.547 2.520 nonbonded pdb=" N VAL H 82 " pdb=" O THR J 81 " model vdw 2.547 2.520 ... (remaining 33182 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' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.50 max=1.00 mean=0.99 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: 0.670 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: 0.000 Extract box with map and model: 3.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.730 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 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 : 0.024 0.101 3900 Z= 1.627 Angle : 1.403 6.343 5290 Z= 0.831 Chirality : 0.088 0.222 710 Planarity : 0.008 0.028 660 Dihedral : 7.442 31.218 1290 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.26), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.20), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS B 50 TYR 0.027 0.011 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.398 Fit side-chains REVERT: A 80 LYS cc_start: 0.7607 (tttt) cc_final: 0.7045 (pttm) REVERT: B 80 LYS cc_start: 0.7372 (tttt) cc_final: 0.6660 (tmmt) REVERT: C 65 ASN cc_start: 0.6524 (m-40) cc_final: 0.6315 (m-40) REVERT: E 65 ASN cc_start: 0.6603 (m-40) cc_final: 0.6356 (m-40) REVERT: F 65 ASN cc_start: 0.6373 (m-40) cc_final: 0.5989 (m-40) REVERT: G 57 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6108 (mp0) REVERT: G 65 ASN cc_start: 0.6459 (m-40) cc_final: 0.6230 (m110) REVERT: I 50 HIS cc_start: 0.6096 (m-70) cc_final: 0.5799 (p90) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1277 time to fit residues: 16.0755 Evaluate side-chains 82 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3900 Z= 0.476 Angle : 0.865 5.686 5290 Z= 0.494 Chirality : 0.052 0.192 710 Planarity : 0.004 0.015 660 Dihedral : 6.732 22.778 580 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.82 % Allowed : 5.64 % Favored : 91.54 % 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: -1.95 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 50 TYR 0.013 0.003 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 0.463 Fit side-chains REVERT: A 80 LYS cc_start: 0.7477 (tttt) cc_final: 0.6765 (pttp) REVERT: B 80 LYS cc_start: 0.7414 (tttt) cc_final: 0.6623 (pttm) REVERT: H 39 TYR cc_start: 0.7487 (t80) cc_final: 0.7119 (t80) outliers start: 11 outliers final: 10 residues processed: 117 average time/residue: 0.1504 time to fit residues: 21.8675 Evaluate side-chains 107 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3900 Z= 0.231 Angle : 0.606 4.726 5290 Z= 0.359 Chirality : 0.050 0.185 710 Planarity : 0.002 0.012 660 Dihedral : 5.824 19.281 580 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.13 % Allowed : 10.26 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.30), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 TYR 0.009 0.002 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7533 (tttt) cc_final: 0.6848 (pttp) REVERT: B 80 LYS cc_start: 0.7324 (tttt) cc_final: 0.6677 (pttp) REVERT: D 39 TYR cc_start: 0.7499 (t80) cc_final: 0.7102 (t80) REVERT: E 80 LYS cc_start: 0.7144 (tttt) cc_final: 0.6867 (tttt) REVERT: H 39 TYR cc_start: 0.7317 (t80) cc_final: 0.7075 (t80) outliers start: 20 outliers final: 14 residues processed: 110 average time/residue: 0.1136 time to fit residues: 16.3296 Evaluate side-chains 111 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 0.0980 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3900 Z= 0.318 Angle : 0.647 4.876 5290 Z= 0.380 Chirality : 0.051 0.176 710 Planarity : 0.003 0.013 660 Dihedral : 5.838 17.152 580 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 5.64 % Allowed : 11.79 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.30), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 50 TYR 0.012 0.002 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7439 (tttt) cc_final: 0.7113 (pttp) REVERT: B 80 LYS cc_start: 0.7223 (tttt) cc_final: 0.6890 (pttp) REVERT: E 80 LYS cc_start: 0.7154 (tttt) cc_final: 0.6462 (tppt) REVERT: F 80 LYS cc_start: 0.6640 (tttt) cc_final: 0.6436 (tttt) REVERT: G 80 LYS cc_start: 0.6839 (tttt) cc_final: 0.6447 (tttt) REVERT: H 39 TYR cc_start: 0.7266 (t80) cc_final: 0.7016 (t80) REVERT: I 80 LYS cc_start: 0.6832 (tptm) cc_final: 0.6507 (tppt) outliers start: 22 outliers final: 17 residues processed: 108 average time/residue: 0.1215 time to fit residues: 17.0614 Evaluate side-chains 107 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3900 Z= 0.298 Angle : 0.611 4.661 5290 Z= 0.358 Chirality : 0.049 0.174 710 Planarity : 0.002 0.010 660 Dihedral : 5.729 16.222 580 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 7.44 % Allowed : 14.10 % 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: -2.31 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS H 50 TYR 0.009 0.002 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 0.409 Fit side-chains REVERT: E 80 LYS cc_start: 0.6920 (tttt) cc_final: 0.6492 (mttm) REVERT: F 80 LYS cc_start: 0.6831 (tttt) cc_final: 0.6093 (tttt) REVERT: H 42 SER cc_start: 0.8952 (t) cc_final: 0.8672 (t) REVERT: J 80 LYS cc_start: 0.7296 (tttt) cc_final: 0.6946 (mttt) outliers start: 29 outliers final: 23 residues processed: 110 average time/residue: 0.1119 time to fit residues: 16.2576 Evaluate side-chains 114 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 40 optimal weight: 0.0370 chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 2.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3900 Z= 0.283 Angle : 0.594 5.241 5290 Z= 0.351 Chirality : 0.049 0.168 710 Planarity : 0.002 0.012 660 Dihedral : 5.589 16.198 580 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 8.46 % Allowed : 15.64 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 50 TYR 0.010 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 96 time to evaluate : 0.381 Fit side-chains REVERT: E 80 LYS cc_start: 0.7100 (tttt) cc_final: 0.6864 (mttm) REVERT: F 80 LYS cc_start: 0.6829 (tttt) cc_final: 0.6232 (tttt) REVERT: H 42 SER cc_start: 0.8894 (t) cc_final: 0.8607 (t) REVERT: H 80 LYS cc_start: 0.6613 (tttt) cc_final: 0.6312 (mttt) REVERT: J 80 LYS cc_start: 0.7192 (tttt) cc_final: 0.6602 (tptt) outliers start: 33 outliers final: 28 residues processed: 116 average time/residue: 0.1031 time to fit residues: 15.9792 Evaluate side-chains 123 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.0270 chunk 32 optimal weight: 1.9990 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3900 Z= 0.204 Angle : 0.528 4.742 5290 Z= 0.314 Chirality : 0.049 0.137 710 Planarity : 0.002 0.009 660 Dihedral : 5.257 16.305 580 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 8.21 % Allowed : 15.38 % Favored : 76.41 % 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: -2.40 (0.30), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 TYR 0.006 0.001 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 0.414 Fit side-chains REVERT: H 42 SER cc_start: 0.8916 (t) cc_final: 0.8671 (t) REVERT: J 80 LYS cc_start: 0.7224 (tttt) cc_final: 0.6898 (mttt) outliers start: 32 outliers final: 27 residues processed: 116 average time/residue: 0.1180 time to fit residues: 17.9699 Evaluate side-chains 122 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3900 Z= 0.317 Angle : 0.608 5.542 5290 Z= 0.356 Chirality : 0.050 0.151 710 Planarity : 0.003 0.016 660 Dihedral : 5.544 18.756 580 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 8.72 % Allowed : 16.92 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 50 TYR 0.011 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 96 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: D 80 LYS cc_start: 0.7166 (tttt) cc_final: 0.6916 (mttm) REVERT: F 80 LYS cc_start: 0.6944 (tttt) cc_final: 0.6645 (tttt) REVERT: H 42 SER cc_start: 0.8887 (t) cc_final: 0.8611 (t) REVERT: H 80 LYS cc_start: 0.7517 (mttt) cc_final: 0.6324 (ttmt) REVERT: J 80 LYS cc_start: 0.7117 (tttt) cc_final: 0.6646 (tttt) outliers start: 34 outliers final: 28 residues processed: 116 average time/residue: 0.1250 time to fit residues: 19.3880 Evaluate side-chains 122 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 0.1980 chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 0.6748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3900 Z= 0.358 Angle : 0.640 5.502 5290 Z= 0.371 Chirality : 0.050 0.168 710 Planarity : 0.003 0.013 660 Dihedral : 5.881 19.005 580 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 7.95 % Allowed : 17.44 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 50 TYR 0.012 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 0.404 Fit side-chains REVERT: F 80 LYS cc_start: 0.7029 (tttt) cc_final: 0.6472 (mttt) REVERT: H 42 SER cc_start: 0.8931 (t) cc_final: 0.8687 (t) REVERT: I 88 ILE cc_start: 0.6548 (pt) cc_final: 0.6246 (pt) outliers start: 31 outliers final: 31 residues processed: 108 average time/residue: 0.1080 time to fit residues: 15.4221 Evaluate side-chains 121 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.6872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3900 Z= 0.234 Angle : 0.538 4.634 5290 Z= 0.319 Chirality : 0.049 0.140 710 Planarity : 0.002 0.012 660 Dihedral : 5.397 18.709 580 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 8.21 % Allowed : 18.21 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 TYR 0.007 0.001 TYR F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 0.355 Fit side-chains REVERT: F 80 LYS cc_start: 0.6748 (tttt) cc_final: 0.6285 (mttt) REVERT: G 80 LYS cc_start: 0.6723 (tttt) cc_final: 0.6382 (mttt) REVERT: H 42 SER cc_start: 0.8899 (t) cc_final: 0.8668 (t) REVERT: H 80 LYS cc_start: 0.7584 (mttt) cc_final: 0.6490 (ttmt) REVERT: J 80 LYS cc_start: 0.7233 (tttt) cc_final: 0.7018 (mttt) outliers start: 32 outliers final: 30 residues processed: 114 average time/residue: 0.1192 time to fit residues: 17.7660 Evaluate side-chains 128 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 0.0570 chunk 34 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.220613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.201471 restraints weight = 5740.813| |-----------------------------------------------------------------------------| r_work (start): 0.4651 rms_B_bonded: 3.40 r_work: 0.4544 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4545 r_free = 0.4545 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4506 r_free = 0.4506 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 3900 Z= 0.377 Angle : 0.651 7.140 5290 Z= 0.375 Chirality : 0.051 0.167 710 Planarity : 0.003 0.013 660 Dihedral : 5.848 20.157 580 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 7.69 % Allowed : 18.46 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.31), residues: 560 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 50 TYR 0.012 0.002 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1262.66 seconds wall clock time: 23 minutes 36.15 seconds (1416.15 seconds total)