Starting phenix.real_space_refine on Wed Mar 4 17:03:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pf6_13369/03_2026/7pf6_13369.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pf6_13369/03_2026/7pf6_13369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pf6_13369/03_2026/7pf6_13369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pf6_13369/03_2026/7pf6_13369.map" model { file = "/net/cci-nas-00/data/ceres_data/7pf6_13369/03_2026/7pf6_13369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pf6_13369/03_2026/7pf6_13369.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 334 5.49 5 S 10 5.16 5 C 7420 2.51 5 N 2528 2.21 5 O 3178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13470 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3405 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "J" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3442 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 3.32, per 1000 atoms: 0.25 Number of scatterers: 13470 At special positions: 0 Unit cell: (118.65, 149.1, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 334 15.00 O 3178 8.00 N 2528 7.00 C 7420 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 491.4 milliseconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 69.9% alpha, 2.8% beta 167 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.681A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.815A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.759A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.144A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.621A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.514A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.619A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.689A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.834A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.470A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 101 removed outlier: 3.513A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.856A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 51 removed outlier: 3.835A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 69 Processing helix chain 'U' and resid 75 through 90 removed outlier: 3.884A pdb=" N GLY U 90 " --> pdb=" O LEU U 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.789A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.492A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.023A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.367A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'U' and resid 92 through 94 431 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 428 hydrogen bonds 852 hydrogen bond angles 0 basepair planarities 167 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2463 1.33 - 1.45: 4932 1.45 - 1.57: 6305 1.57 - 1.70: 666 1.70 - 1.82: 20 Bond restraints: 14386 Sorted by residual: bond pdb=" C3' DG J 610 " pdb=" O3' DG J 610 " ideal model delta sigma weight residual 1.422 1.524 -0.102 3.00e-02 1.11e+03 1.15e+01 bond pdb=" C3' DT I 167 " pdb=" O3' DT I 167 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C3' DG J 675 " pdb=" O3' DG J 675 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.72e+00 bond pdb=" C ASN C 110 " pdb=" N ILE C 111 " ideal model delta sigma weight residual 1.331 1.307 0.023 1.27e-02 6.20e+03 3.40e+00 bond pdb=" CG1 ILE E 130 " pdb=" CD1 ILE E 130 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.09e+00 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 20808 5.95 - 11.89: 42 11.89 - 17.84: 0 17.84 - 23.79: 2 23.79 - 29.73: 1 Bond angle restraints: 20853 Sorted by residual: angle pdb=" O3' DG J 610 " pdb=" P DG J 611 " pdb=" OP2 DG J 611 " ideal model delta sigma weight residual 108.00 78.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" O3' DG J 610 " pdb=" P DG J 611 " pdb=" OP1 DG J 611 " ideal model delta sigma weight residual 108.00 85.49 22.51 3.00e+00 1.11e-01 5.63e+01 angle pdb=" OP1 DG J 611 " pdb=" P DG J 611 " pdb=" OP2 DG J 611 " ideal model delta sigma weight residual 120.00 141.43 -21.43 3.00e+00 1.11e-01 5.10e+01 angle pdb=" N ILE G 79 " pdb=" CA ILE G 79 " pdb=" C ILE G 79 " ideal model delta sigma weight residual 108.45 102.43 6.02 1.20e+00 6.94e-01 2.52e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.02 119.47 -8.45 1.86e+00 2.89e-01 2.07e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 6024 34.71 - 69.42: 1725 69.42 - 104.13: 44 104.13 - 138.84: 3 138.84 - 173.55: 3 Dihedral angle restraints: 7799 sinusoidal: 5368 harmonic: 2431 Sorted by residual: dihedral pdb=" CA GLN G 24 " pdb=" C GLN G 24 " pdb=" N PHE G 25 " pdb=" CA PHE G 25 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ILE H 54 " pdb=" C ILE H 54 " pdb=" N SER H 55 " pdb=" CA SER H 55 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 2375 0.384 - 0.768: 0 0.768 - 1.152: 0 1.152 - 1.535: 0 1.535 - 1.919: 1 Chirality restraints: 2376 Sorted by residual: chirality pdb=" P DG J 611 " pdb=" OP1 DG J 611 " pdb=" OP2 DG J 611 " pdb=" O5' DG J 611 " both_signs ideal model delta sigma weight residual True 2.35 0.43 1.92 2.00e-01 2.50e+01 9.21e+01 chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2373 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO G 80 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 30 " 0.034 2.00e-02 2.50e+03 1.75e-02 6.88e+00 pdb=" N1 DC I 30 " -0.033 2.00e-02 2.50e+03 pdb=" C2 DC I 30 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 30 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 30 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 30 " 0.012 2.00e-02 2.50e+03 pdb=" N4 DC I 30 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 30 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DC I 30 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO H 103 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.035 5.00e-02 4.00e+02 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2943 2.79 - 3.32: 12785 3.32 - 3.85: 29386 3.85 - 4.37: 32078 4.37 - 4.90: 44329 Nonbonded interactions: 121521 Sorted by model distance: nonbonded pdb=" NZ LYS A 37 " pdb=" OP1 DC J 726 " model vdw 2.268 3.120 nonbonded pdb=" OG SER G 40 " pdb=" O ARG G 42 " model vdw 2.291 3.040 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.309 3.040 nonbonded pdb=" O GLU F 74 " pdb=" NH2 ARG H 92 " model vdw 2.313 3.120 nonbonded pdb=" OG SER F 47 " pdb=" OP1 DC J 662 " model vdw 2.314 3.040 ... (remaining 121516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.510 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.006 0.102 14386 Z= 0.280 Angle : 0.986 29.733 20853 Z= 0.539 Chirality : 0.064 1.919 2376 Planarity : 0.008 0.084 1478 Dihedral : 29.581 173.553 6233 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.26), residues: 825 helix: -0.26 (0.20), residues: 573 sheet: None (None), residues: 0 loop : -0.72 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 99 TYR 0.034 0.004 TYR E 54 PHE 0.032 0.003 PHE E 104 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00625 (14386) covalent geometry : angle 0.98595 (20853) hydrogen bonds : bond 0.11346 ( 859) hydrogen bonds : angle 4.71288 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.6986 (mm) cc_final: 0.5837 (mm) REVERT: A 90 MET cc_start: 0.8665 (mmp) cc_final: 0.8320 (mmp) REVERT: A 93 GLN cc_start: 0.8953 (tt0) cc_final: 0.8694 (tp40) REVERT: A 94 GLU cc_start: 0.8981 (mp0) cc_final: 0.8595 (pm20) REVERT: B 68 ASP cc_start: 0.9022 (m-30) cc_final: 0.8784 (m-30) REVERT: C 62 ILE cc_start: 0.9108 (pt) cc_final: 0.8908 (pt) REVERT: C 73 ASN cc_start: 0.8677 (t0) cc_final: 0.8361 (p0) REVERT: D 108 LYS cc_start: 0.9237 (mppt) cc_final: 0.8997 (mtmm) REVERT: E 104 PHE cc_start: 0.8634 (m-80) cc_final: 0.8386 (m-80) REVERT: F 62 LEU cc_start: 0.9648 (mt) cc_final: 0.9444 (mt) REVERT: F 63 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7914 (tm-30) REVERT: G 36 LYS cc_start: 0.9070 (mppt) cc_final: 0.8656 (mppt) REVERT: G 64 GLU cc_start: 0.8945 (tp30) cc_final: 0.8717 (tp30) REVERT: G 95 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8448 (mmmt) REVERT: H 47 GLN cc_start: 0.9116 (mt0) cc_final: 0.8805 (mt0) REVERT: H 85 LYS cc_start: 0.9417 (mppt) cc_final: 0.9120 (tptp) REVERT: H 106 LEU cc_start: 0.9607 (tp) cc_final: 0.9403 (tp) REVERT: H 113 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8417 (mm-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1144 time to fit residues: 28.9614 Evaluate side-chains 120 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN E 93 GLN E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.056601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.047147 restraints weight = 119622.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.048328 restraints weight = 72874.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.049107 restraints weight = 51680.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.049623 restraints weight = 40696.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.049958 restraints weight = 34413.923| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14386 Z= 0.172 Angle : 0.703 26.572 20853 Z= 0.393 Chirality : 0.055 2.024 2376 Planarity : 0.005 0.062 1478 Dihedral : 32.462 171.319 4581 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.15 % Allowed : 9.96 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.27), residues: 825 helix: 0.92 (0.21), residues: 579 sheet: None (None), residues: 0 loop : -0.48 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 72 TYR 0.023 0.002 TYR F 88 PHE 0.011 0.001 PHE H 65 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00367 (14386) covalent geometry : angle 0.70286 (20853) hydrogen bonds : bond 0.04576 ( 859) hydrogen bonds : angle 3.38793 ( 2133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.6866 (mm) cc_final: 0.5557 (mm) REVERT: A 93 GLN cc_start: 0.9030 (tt0) cc_final: 0.8820 (tp40) REVERT: B 85 ASP cc_start: 0.8479 (m-30) cc_final: 0.8239 (m-30) REVERT: D 46 LYS cc_start: 0.8510 (mmtt) cc_final: 0.7747 (mmmt) REVERT: E 77 ASP cc_start: 0.9093 (m-30) cc_final: 0.8679 (t70) REVERT: E 97 GLU cc_start: 0.8036 (pt0) cc_final: 0.7774 (pt0) REVERT: E 104 PHE cc_start: 0.8697 (m-80) cc_final: 0.8481 (m-80) REVERT: E 108 ASN cc_start: 0.8693 (m-40) cc_final: 0.8452 (m110) REVERT: F 63 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7881 (tm-30) REVERT: F 74 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8468 (tm-30) REVERT: G 36 LYS cc_start: 0.8809 (mppt) cc_final: 0.8526 (mmtm) REVERT: G 95 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8480 (mmmt) REVERT: H 47 GLN cc_start: 0.9094 (mt0) cc_final: 0.8832 (mt0) REVERT: H 109 HIS cc_start: 0.9430 (m170) cc_final: 0.9031 (m170) outliers start: 8 outliers final: 4 residues processed: 160 average time/residue: 0.1059 time to fit residues: 25.3563 Evaluate side-chains 119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 8 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 84 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.056832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.047855 restraints weight = 119543.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.049031 restraints weight = 70035.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.049806 restraints weight = 48658.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.050304 restraints weight = 37673.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.050667 restraints weight = 31580.701| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14386 Z= 0.165 Angle : 0.683 26.261 20853 Z= 0.381 Chirality : 0.055 2.017 2376 Planarity : 0.005 0.061 1478 Dihedral : 32.198 170.970 4581 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.30 % Allowed : 13.42 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.28), residues: 825 helix: 1.25 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -0.38 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.021 0.002 TYR B 88 PHE 0.008 0.001 PHE G 25 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00355 (14386) covalent geometry : angle 0.68288 (20853) hydrogen bonds : bond 0.04130 ( 859) hydrogen bonds : angle 3.20116 ( 2133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.6762 (mm) cc_final: 0.5412 (mm) REVERT: A 105 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8432 (mt-10) REVERT: B 85 ASP cc_start: 0.8557 (m-30) cc_final: 0.8279 (m-30) REVERT: D 46 LYS cc_start: 0.8361 (mmtt) cc_final: 0.7584 (mmmt) REVERT: D 52 THR cc_start: 0.7666 (m) cc_final: 0.7426 (m) REVERT: D 71 GLU cc_start: 0.8237 (pp20) cc_final: 0.8030 (pp20) REVERT: E 77 ASP cc_start: 0.9098 (m-30) cc_final: 0.8634 (t0) REVERT: F 63 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7940 (tm-30) REVERT: F 74 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8458 (tm-30) REVERT: G 36 LYS cc_start: 0.8781 (mppt) cc_final: 0.8500 (mmtm) REVERT: G 79 ILE cc_start: 0.9502 (tp) cc_final: 0.9132 (tp) REVERT: G 95 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8554 (mmmt) REVERT: H 47 GLN cc_start: 0.9012 (mt0) cc_final: 0.8788 (mt0) outliers start: 9 outliers final: 6 residues processed: 148 average time/residue: 0.1111 time to fit residues: 24.2088 Evaluate side-chains 123 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.050761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.041748 restraints weight = 124827.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.042816 restraints weight = 75221.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.043508 restraints weight = 53355.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.044000 restraints weight = 42000.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.044318 restraints weight = 35312.517| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 14386 Z= 0.310 Angle : 0.780 27.892 20853 Z= 0.438 Chirality : 0.059 2.045 2376 Planarity : 0.006 0.060 1478 Dihedral : 32.781 167.534 4581 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.02 % Allowed : 16.74 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.28), residues: 825 helix: 0.89 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 53 TYR 0.030 0.003 TYR D 40 PHE 0.026 0.002 PHE E 104 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00669 (14386) covalent geometry : angle 0.77977 (20853) hydrogen bonds : bond 0.08671 ( 859) hydrogen bonds : angle 3.89038 ( 2133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.9528 (OUTLIER) cc_final: 0.9229 (mp10) REVERT: B 44 LYS cc_start: 0.7955 (pttt) cc_final: 0.7031 (pptt) REVERT: D 46 LYS cc_start: 0.8663 (mmtt) cc_final: 0.7605 (mmmt) REVERT: D 71 GLU cc_start: 0.8327 (pp20) cc_final: 0.8104 (pp20) REVERT: E 77 ASP cc_start: 0.9172 (m-30) cc_final: 0.8720 (t0) REVERT: E 108 ASN cc_start: 0.8819 (m-40) cc_final: 0.8584 (m-40) REVERT: F 63 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7956 (tm-30) REVERT: F 74 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8405 (tm-30) REVERT: G 36 LYS cc_start: 0.8735 (mppt) cc_final: 0.8423 (mmtm) REVERT: G 95 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8616 (mmmt) REVERT: H 47 GLN cc_start: 0.9115 (mt0) cc_final: 0.8793 (mt0) REVERT: H 99 ARG cc_start: 0.9545 (mmm-85) cc_final: 0.9272 (mmm-85) REVERT: H 109 HIS cc_start: 0.9587 (m170) cc_final: 0.9326 (m170) outliers start: 14 outliers final: 8 residues processed: 129 average time/residue: 0.1070 time to fit residues: 20.7908 Evaluate side-chains 118 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 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 = 0.3741 r_free = 0.3741 target = 0.053136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.043826 restraints weight = 124816.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.044953 restraints weight = 74260.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.045693 restraints weight = 52447.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.046208 restraints weight = 41340.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.046549 restraints weight = 34795.936| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14386 Z= 0.186 Angle : 0.710 26.940 20853 Z= 0.398 Chirality : 0.055 1.982 2376 Planarity : 0.004 0.059 1478 Dihedral : 32.475 168.522 4581 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.72 % Allowed : 18.61 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.28), residues: 825 helix: 1.13 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.34 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.034 0.002 TYR F 88 PHE 0.045 0.002 PHE E 104 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00401 (14386) covalent geometry : angle 0.70956 (20853) hydrogen bonds : bond 0.04844 ( 859) hydrogen bonds : angle 3.42664 ( 2133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.7953 (pttt) cc_final: 0.7425 (pttp) REVERT: D 46 LYS cc_start: 0.8626 (mmtt) cc_final: 0.7723 (mmmt) REVERT: D 52 THR cc_start: 0.8000 (m) cc_final: 0.7635 (m) REVERT: D 71 GLU cc_start: 0.8296 (pp20) cc_final: 0.8003 (pp20) REVERT: D 105 GLU cc_start: 0.9328 (tm-30) cc_final: 0.9067 (tm-30) REVERT: E 77 ASP cc_start: 0.9204 (m-30) cc_final: 0.8710 (t0) REVERT: E 79 LYS cc_start: 0.7863 (tmtt) cc_final: 0.7242 (tmtt) REVERT: E 104 PHE cc_start: 0.8915 (m-80) cc_final: 0.8571 (m-80) REVERT: F 63 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8043 (tm-30) REVERT: F 74 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8493 (tm-30) REVERT: G 36 LYS cc_start: 0.8826 (mppt) cc_final: 0.8564 (mmtm) REVERT: G 95 LYS cc_start: 0.8836 (mmmt) cc_final: 0.8611 (mmmt) REVERT: H 47 GLN cc_start: 0.9052 (mt0) cc_final: 0.8787 (mt0) REVERT: H 99 ARG cc_start: 0.9519 (mmm-85) cc_final: 0.9290 (mtp85) REVERT: H 109 HIS cc_start: 0.9587 (m170) cc_final: 0.9256 (m170) outliers start: 5 outliers final: 4 residues processed: 136 average time/residue: 0.1153 time to fit residues: 23.0378 Evaluate side-chains 124 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.053937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.044638 restraints weight = 123018.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.045781 restraints weight = 73251.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.046557 restraints weight = 51701.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.047039 restraints weight = 40408.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.047404 restraints weight = 34245.887| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14386 Z= 0.174 Angle : 0.705 26.998 20853 Z= 0.390 Chirality : 0.054 1.966 2376 Planarity : 0.004 0.055 1478 Dihedral : 32.220 164.827 4581 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.73 % Allowed : 20.63 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.28), residues: 825 helix: 1.16 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -0.43 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.035 0.002 TYR D 40 PHE 0.041 0.002 PHE E 104 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00376 (14386) covalent geometry : angle 0.70453 (20853) hydrogen bonds : bond 0.04445 ( 859) hydrogen bonds : angle 3.34531 ( 2133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.8039 (pttt) cc_final: 0.7652 (ttpt) REVERT: C 91 GLU cc_start: 0.7221 (tp30) cc_final: 0.6921 (tp30) REVERT: D 46 LYS cc_start: 0.8435 (mmtt) cc_final: 0.7561 (mmmt) REVERT: D 52 THR cc_start: 0.7986 (m) cc_final: 0.7635 (m) REVERT: D 71 GLU cc_start: 0.8351 (pp20) cc_final: 0.8044 (pp20) REVERT: E 77 ASP cc_start: 0.9215 (m-30) cc_final: 0.8688 (t0) REVERT: E 79 LYS cc_start: 0.7829 (tmtt) cc_final: 0.7204 (tmtt) REVERT: E 104 PHE cc_start: 0.8822 (m-80) cc_final: 0.8400 (m-80) REVERT: E 120 MET cc_start: 0.1868 (mtt) cc_final: 0.1667 (mtt) REVERT: F 63 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8168 (tm-30) REVERT: F 74 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8511 (tm-30) REVERT: G 36 LYS cc_start: 0.8802 (mppt) cc_final: 0.8591 (mmtm) REVERT: H 47 GLN cc_start: 0.8999 (mt0) cc_final: 0.8731 (mt0) REVERT: H 99 ARG cc_start: 0.9520 (mmm-85) cc_final: 0.9286 (mtp85) outliers start: 12 outliers final: 9 residues processed: 142 average time/residue: 0.1212 time to fit residues: 25.0208 Evaluate side-chains 128 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN C 112 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.049758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.040897 restraints weight = 125969.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.041940 restraints weight = 75669.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.042627 restraints weight = 53548.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.043108 restraints weight = 42091.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.043426 restraints weight = 35362.947| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 14386 Z= 0.301 Angle : 0.794 28.031 20853 Z= 0.441 Chirality : 0.057 1.982 2376 Planarity : 0.006 0.059 1478 Dihedral : 32.580 168.686 4581 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.30 % Allowed : 21.79 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.28), residues: 825 helix: 0.73 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.52 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 86 TYR 0.031 0.003 TYR F 88 PHE 0.034 0.002 PHE E 104 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00652 (14386) covalent geometry : angle 0.79354 (20853) hydrogen bonds : bond 0.08577 ( 859) hydrogen bonds : angle 3.88503 ( 2133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.9282 (mp10) REVERT: D 40 TYR cc_start: 0.7272 (m-80) cc_final: 0.7019 (m-10) REVERT: D 46 LYS cc_start: 0.8640 (mmtt) cc_final: 0.7559 (mmmt) REVERT: D 52 THR cc_start: 0.8160 (m) cc_final: 0.7871 (m) REVERT: D 71 GLU cc_start: 0.8372 (pp20) cc_final: 0.8093 (pp20) REVERT: E 77 ASP cc_start: 0.9193 (m-30) cc_final: 0.8638 (t0) REVERT: E 79 LYS cc_start: 0.8160 (tmtt) cc_final: 0.7585 (tmtt) REVERT: F 63 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8208 (tm-30) REVERT: F 74 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8543 (tm-30) REVERT: G 36 LYS cc_start: 0.8739 (mppt) cc_final: 0.8481 (mmtm) REVERT: H 47 GLN cc_start: 0.9055 (mt0) cc_final: 0.8717 (mt0) REVERT: H 83 TYR cc_start: 0.7604 (m-10) cc_final: 0.7402 (m-80) REVERT: H 99 ARG cc_start: 0.9532 (mmm-85) cc_final: 0.9088 (mmm-85) outliers start: 9 outliers final: 5 residues processed: 121 average time/residue: 0.1117 time to fit residues: 20.0740 Evaluate side-chains 119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain H residue 82 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 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 = 0.3619 r_free = 0.3619 target = 0.048322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.039644 restraints weight = 127840.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.040649 restraints weight = 77366.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.041327 restraints weight = 55096.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.041778 restraints weight = 43407.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.042068 restraints weight = 36711.381| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14386 Z= 0.288 Angle : 0.818 27.642 20853 Z= 0.453 Chirality : 0.058 1.946 2376 Planarity : 0.006 0.056 1478 Dihedral : 32.818 168.328 4581 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.30 % Allowed : 22.22 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.28), residues: 825 helix: 0.49 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.68 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 86 TYR 0.039 0.003 TYR F 88 PHE 0.020 0.002 PHE B 100 HIS 0.011 0.002 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00621 (14386) covalent geometry : angle 0.81827 (20853) hydrogen bonds : bond 0.07576 ( 859) hydrogen bonds : angle 4.03208 ( 2133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.8729 (pttt) cc_final: 0.8327 (pttp) REVERT: D 46 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8184 (mmtm) REVERT: D 62 MET cc_start: 0.7993 (mmp) cc_final: 0.7774 (mmp) REVERT: D 71 GLU cc_start: 0.8395 (pp20) cc_final: 0.8122 (pp20) REVERT: E 79 LYS cc_start: 0.8307 (tmtt) cc_final: 0.8013 (tmmt) REVERT: F 63 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8154 (tm-30) REVERT: F 74 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8595 (tm-30) REVERT: G 57 TYR cc_start: 0.8716 (t80) cc_final: 0.8438 (t80) REVERT: H 85 LYS cc_start: 0.9576 (pttp) cc_final: 0.9128 (tptp) REVERT: H 99 ARG cc_start: 0.9537 (mmm-85) cc_final: 0.9130 (mmm-85) outliers start: 9 outliers final: 5 residues processed: 130 average time/residue: 0.1182 time to fit residues: 22.4949 Evaluate side-chains 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.048066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.039192 restraints weight = 131147.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.040241 restraints weight = 76766.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.040940 restraints weight = 53818.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.041408 restraints weight = 42097.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.041709 restraints weight = 35474.442| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14386 Z= 0.269 Angle : 0.818 27.977 20853 Z= 0.452 Chirality : 0.057 1.952 2376 Planarity : 0.006 0.058 1478 Dihedral : 32.836 168.999 4581 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.30 % Allowed : 23.67 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.28), residues: 825 helix: 0.48 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.76 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 86 TYR 0.056 0.003 TYR F 88 PHE 0.013 0.002 PHE H 70 HIS 0.007 0.002 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00585 (14386) covalent geometry : angle 0.81797 (20853) hydrogen bonds : bond 0.07400 ( 859) hydrogen bonds : angle 4.02411 ( 2133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9055 (pt0) cc_final: 0.8728 (pm20) REVERT: D 71 GLU cc_start: 0.8427 (pp20) cc_final: 0.8134 (pp20) REVERT: E 79 LYS cc_start: 0.8344 (tmtt) cc_final: 0.8083 (tmmt) REVERT: E 106 ASP cc_start: 0.8814 (m-30) cc_final: 0.8562 (m-30) REVERT: F 63 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8169 (tm-30) REVERT: F 74 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8600 (tm-30) REVERT: G 57 TYR cc_start: 0.8684 (t80) cc_final: 0.8449 (t80) REVERT: H 85 LYS cc_start: 0.9554 (pttp) cc_final: 0.8957 (tptp) REVERT: H 99 ARG cc_start: 0.9540 (mmm-85) cc_final: 0.9160 (mmm-85) outliers start: 9 outliers final: 8 residues processed: 120 average time/residue: 0.1173 time to fit residues: 20.6733 Evaluate side-chains 115 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 75 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN C 38 ASN C 84 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.051336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.042315 restraints weight = 126086.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.043394 restraints weight = 74335.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.044118 restraints weight = 52249.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.044582 restraints weight = 40861.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.044919 restraints weight = 34639.559| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14386 Z= 0.184 Angle : 0.779 27.302 20853 Z= 0.429 Chirality : 0.056 1.934 2376 Planarity : 0.005 0.055 1478 Dihedral : 32.555 167.713 4581 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.87 % Allowed : 24.24 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.28), residues: 825 helix: 0.70 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.73 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 52 TYR 0.040 0.002 TYR A 54 PHE 0.010 0.001 PHE H 70 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00399 (14386) covalent geometry : angle 0.77913 (20853) hydrogen bonds : bond 0.04579 ( 859) hydrogen bonds : angle 3.68791 ( 2133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.8728 (pttt) cc_final: 0.7863 (pptt) REVERT: C 84 GLN cc_start: 0.6087 (OUTLIER) cc_final: 0.4559 (tm-30) REVERT: D 71 GLU cc_start: 0.8289 (pp20) cc_final: 0.7996 (pp20) REVERT: E 77 ASP cc_start: 0.9262 (m-30) cc_final: 0.8907 (p0) REVERT: E 79 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7115 (tmmt) REVERT: E 106 ASP cc_start: 0.8773 (m-30) cc_final: 0.8503 (m-30) REVERT: F 63 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8112 (tm-30) REVERT: F 68 ASP cc_start: 0.9212 (m-30) cc_final: 0.8687 (p0) REVERT: F 74 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8510 (tm-30) REVERT: F 86 VAL cc_start: 0.8413 (t) cc_final: 0.8129 (t) REVERT: H 85 LYS cc_start: 0.9538 (pttp) cc_final: 0.8929 (tptp) REVERT: H 99 ARG cc_start: 0.9521 (mmm-85) cc_final: 0.9169 (mmm-85) outliers start: 6 outliers final: 4 residues processed: 130 average time/residue: 0.1177 time to fit residues: 22.0870 Evaluate side-chains 119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.050674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.041727 restraints weight = 126898.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.042786 restraints weight = 74853.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.043507 restraints weight = 52691.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.043994 restraints weight = 41350.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.044316 restraints weight = 34819.067| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14386 Z= 0.195 Angle : 0.785 26.669 20853 Z= 0.433 Chirality : 0.057 2.014 2376 Planarity : 0.005 0.050 1478 Dihedral : 32.486 169.188 4581 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.87 % Allowed : 25.97 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.28), residues: 825 helix: 0.71 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.73 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 32 TYR 0.030 0.002 TYR H 83 PHE 0.010 0.002 PHE H 70 HIS 0.007 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00428 (14386) covalent geometry : angle 0.78536 (20853) hydrogen bonds : bond 0.04983 ( 859) hydrogen bonds : angle 3.71388 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.62 seconds wall clock time: 40 minutes 4.80 seconds (2404.80 seconds total)