Starting phenix.real_space_refine on Tue Jul 29 02:25:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9be6_44471/07_2025/9be6_44471.cif Found real_map, /net/cci-nas-00/data/ceres_data/9be6_44471/07_2025/9be6_44471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9be6_44471/07_2025/9be6_44471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9be6_44471/07_2025/9be6_44471.map" model { file = "/net/cci-nas-00/data/ceres_data/9be6_44471/07_2025/9be6_44471.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9be6_44471/07_2025/9be6_44471.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.177 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: 5 Type Number sf(0) Gaussians P 253 5.49 5 S 12 5.16 5 C 6227 2.51 5 N 2094 2.21 5 O 2577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11163 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2587 Classifications: {'DNA': 127} Link IDs: {'rna3p': 126} Chain: "J" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2617 Classifications: {'DNA': 127} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 126} Time building chain proxies: 7.65, per 1000 atoms: 0.69 Number of scatterers: 11163 At special positions: 0 Unit cell: (77.469, 121.618, 117.453, 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 12 16.00 P 253 15.00 O 2577 8.00 N 2094 7.00 C 6227 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: 2.85 Conformation dependent library (CDL) restraints added in 794.6 milliseconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 72.8% alpha, 3.2% beta 123 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.523A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.667A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.556A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.604A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.989A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.661A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.699A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.502A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.595A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.635A 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 131 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: 3.955A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.796A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.509A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.722A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.534A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.521A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.637A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.351A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.027A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.327A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 395 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 314 hydrogen bonds 628 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 4.15 Time building geometry restraints manager: 3.40 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: 1994 1.33 - 1.45: 3834 1.45 - 1.57: 5520 1.57 - 1.69: 505 1.69 - 1.81: 22 Bond restraints: 11875 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.470 -0.048 3.00e-02 1.11e+03 2.58e+00 bond pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" C3' DC J 34 " pdb=" C2' DC J 34 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" C3' DA J -38 " pdb=" C2' DA J -38 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.02e+00 ... (remaining 11870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 16307 1.27 - 2.53: 745 2.53 - 3.80: 58 3.80 - 5.06: 12 5.06 - 6.33: 4 Bond angle restraints: 17126 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.53 108.43 5.10 9.80e-01 1.04e+00 2.71e+01 angle pdb=" N GLU E 50 " pdb=" CA GLU E 50 " pdb=" CB GLU E 50 " ideal model delta sigma weight residual 110.39 115.37 -4.98 1.66e+00 3.63e-01 9.01e+00 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 119.51 -6.33 2.37e+00 1.78e-01 7.12e+00 angle pdb=" C ARG E 49 " pdb=" N GLU E 50 " pdb=" CA GLU E 50 " ideal model delta sigma weight residual 120.72 116.50 4.22 1.67e+00 3.59e-01 6.37e+00 angle pdb=" CA VAL E 117 " pdb=" C VAL E 117 " pdb=" N THR E 118 " ideal model delta sigma weight residual 119.31 116.68 2.63 1.15e+00 7.56e-01 5.24e+00 ... (remaining 17121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 5196 33.26 - 66.53: 1288 66.53 - 99.79: 22 99.79 - 133.06: 2 133.06 - 166.32: 1 Dihedral angle restraints: 6509 sinusoidal: 4330 harmonic: 2179 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 53.68 166.32 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" C4' DC I 4 " pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " pdb=" P DC I 5 " ideal model delta sinusoidal sigma weight residual 220.00 104.68 115.32 1 3.50e+01 8.16e-04 1.12e+01 ... (remaining 6506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1414 0.036 - 0.072: 438 0.072 - 0.108: 84 0.108 - 0.143: 16 0.143 - 0.179: 2 Chirality restraints: 1954 Sorted by residual: chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CG LEU A 61 " pdb=" CB LEU A 61 " pdb=" CD1 LEU A 61 " pdb=" CD2 LEU A 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1951 not shown) Planarity restraints: 1289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.022 2.00e-02 2.50e+03 9.27e-03 2.58e+00 pdb=" N9 DG I 26 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.022 2.00e-02 2.50e+03 9.40e-03 2.43e+00 pdb=" N9 DA I -35 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO C 80 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.022 5.00e-02 4.00e+02 ... (remaining 1286 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2266 2.81 - 3.33: 9267 3.33 - 3.85: 20158 3.85 - 4.38: 24761 4.38 - 4.90: 35512 Nonbonded interactions: 91964 Sorted by model distance: nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR D 39 " pdb=" OP2 DG I -52 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DT I 30 " model vdw 2.326 3.040 nonbonded pdb=" O VAL E 46 " pdb=" OE1 GLU E 50 " model vdw 2.356 3.040 ... (remaining 91959 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' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) 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 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 33.180 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.004 0.048 11875 Z= 0.196 Angle : 0.593 6.325 17126 Z= 0.361 Chirality : 0.036 0.179 1954 Planarity : 0.004 0.039 1289 Dihedral : 26.773 166.321 5103 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % 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: 735 helix: 2.32 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.21 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 31 PHE 0.015 0.002 PHE A 78 TYR 0.016 0.002 TYR C 50 ARG 0.005 0.001 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.12698 ( 709) hydrogen bonds : angle 4.24327 ( 1795) covalent geometry : bond 0.00430 (11875) covalent geometry : angle 0.59310 (17126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.886 Fit side-chains REVERT: D 43 LYS cc_start: 0.8299 (mmtt) cc_final: 0.8099 (mmtp) REVERT: D 116 THR cc_start: 0.8460 (t) cc_final: 0.8236 (m) REVERT: F 44 LYS cc_start: 0.8298 (tttm) cc_final: 0.8096 (mtpp) REVERT: G 110 ASN cc_start: 0.8429 (p0) cc_final: 0.8106 (p0) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 1.8239 time to fit residues: 226.8355 Evaluate side-chains 103 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 0.0570 chunk 74 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN G 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.183865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.148644 restraints weight = 11122.183| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 0.68 r_work: 0.3313 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11875 Z= 0.154 Angle : 0.537 6.987 17126 Z= 0.326 Chirality : 0.033 0.122 1954 Planarity : 0.004 0.034 1289 Dihedral : 29.522 166.383 3623 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.60 % Allowed : 7.36 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.72 (0.31), residues: 735 helix: 2.78 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.01 (0.37), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 31 PHE 0.010 0.001 PHE A 78 TYR 0.008 0.001 TYR F 51 ARG 0.004 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.05153 ( 709) hydrogen bonds : angle 2.73355 ( 1795) covalent geometry : bond 0.00324 (11875) covalent geometry : angle 0.53661 (17126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.916 Fit side-chains REVERT: D 43 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7902 (mmtt) REVERT: F 44 LYS cc_start: 0.8785 (tttm) cc_final: 0.8580 (mtpp) REVERT: G 110 ASN cc_start: 0.8757 (p0) cc_final: 0.8491 (p0) outliers start: 10 outliers final: 5 residues processed: 109 average time/residue: 1.8500 time to fit residues: 213.4419 Evaluate side-chains 109 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 90 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 GLN G 38 ASN G 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.182270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146903 restraints weight = 11213.235| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 0.75 r_work: 0.3338 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11875 Z= 0.163 Angle : 0.533 7.404 17126 Z= 0.324 Chirality : 0.034 0.123 1954 Planarity : 0.004 0.032 1289 Dihedral : 29.518 166.730 3623 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.44 % Allowed : 10.88 % Favored : 87.68 % 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: 2.84 (0.31), residues: 735 helix: 2.86 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.99 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 31 PHE 0.012 0.002 PHE A 78 TYR 0.010 0.001 TYR G 50 ARG 0.004 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.05358 ( 709) hydrogen bonds : angle 2.66044 ( 1795) covalent geometry : bond 0.00349 (11875) covalent geometry : angle 0.53346 (17126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.791 Fit side-chains REVERT: D 116 THR cc_start: 0.8277 (t) cc_final: 0.8049 (m) REVERT: F 44 LYS cc_start: 0.8769 (tttm) cc_final: 0.8548 (mtpp) REVERT: H 32 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7094 (mt-10) outliers start: 9 outliers final: 4 residues processed: 114 average time/residue: 1.8847 time to fit residues: 225.9569 Evaluate side-chains 114 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.179297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.140558 restraints weight = 11302.198| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 0.85 r_work: 0.3343 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11875 Z= 0.173 Angle : 0.542 7.735 17126 Z= 0.328 Chirality : 0.034 0.125 1954 Planarity : 0.004 0.032 1289 Dihedral : 29.484 166.853 3623 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.76 % Allowed : 12.00 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.81 (0.31), residues: 735 helix: 2.85 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -0.98 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.012 0.002 PHE A 78 TYR 0.010 0.001 TYR F 51 ARG 0.006 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.05665 ( 709) hydrogen bonds : angle 2.66194 ( 1795) covalent geometry : bond 0.00376 (11875) covalent geometry : angle 0.54164 (17126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.900 Fit side-chains REVERT: D 116 THR cc_start: 0.8102 (t) cc_final: 0.7895 (m) REVERT: E 50 GLU cc_start: 0.8073 (mp0) cc_final: 0.7854 (mp0) REVERT: F 44 LYS cc_start: 0.8864 (tttm) cc_final: 0.8639 (ttmm) REVERT: H 32 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7611 (mt-10) outliers start: 11 outliers final: 6 residues processed: 107 average time/residue: 1.9870 time to fit residues: 223.2921 Evaluate side-chains 112 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.179838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140728 restraints weight = 11234.601| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 0.79 r_work: 0.3372 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11875 Z= 0.156 Angle : 0.531 7.609 17126 Z= 0.323 Chirality : 0.033 0.123 1954 Planarity : 0.003 0.032 1289 Dihedral : 29.474 166.882 3623 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.60 % Allowed : 12.64 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.31), residues: 735 helix: 2.93 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -0.96 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 31 PHE 0.009 0.001 PHE A 78 TYR 0.009 0.001 TYR F 51 ARG 0.003 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.05403 ( 709) hydrogen bonds : angle 2.67057 ( 1795) covalent geometry : bond 0.00328 (11875) covalent geometry : angle 0.53092 (17126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.817 Fit side-chains REVERT: D 116 THR cc_start: 0.8083 (t) cc_final: 0.7875 (m) REVERT: E 50 GLU cc_start: 0.8111 (mp0) cc_final: 0.7874 (mp0) REVERT: F 44 LYS cc_start: 0.8836 (tttm) cc_final: 0.8605 (ttmm) REVERT: H 32 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7638 (mt-10) outliers start: 10 outliers final: 8 residues processed: 107 average time/residue: 1.8592 time to fit residues: 209.4455 Evaluate side-chains 114 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS G 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.172967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.136868 restraints weight = 11248.133| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 0.80 r_work: 0.3263 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11875 Z= 0.322 Angle : 0.679 9.281 17126 Z= 0.399 Chirality : 0.042 0.146 1954 Planarity : 0.006 0.055 1289 Dihedral : 29.845 162.097 3623 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.24 % Allowed : 12.48 % 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 (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: 1.91 (0.30), residues: 735 helix: 2.19 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.37 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS G 31 PHE 0.021 0.003 PHE A 78 TYR 0.014 0.002 TYR E 54 ARG 0.005 0.001 ARG B 78 Details of bonding type rmsd hydrogen bonds : bond 0.08898 ( 709) hydrogen bonds : angle 3.04123 ( 1795) covalent geometry : bond 0.00744 (11875) covalent geometry : angle 0.67878 (17126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.887 Fit side-chains REVERT: A 115 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8655 (mttp) REVERT: C 75 LYS cc_start: 0.8344 (mttt) cc_final: 0.8036 (mttt) REVERT: D 116 THR cc_start: 0.8419 (t) cc_final: 0.8175 (m) REVERT: E 50 GLU cc_start: 0.8117 (mp0) cc_final: 0.7875 (mp0) REVERT: F 44 LYS cc_start: 0.8844 (tttm) cc_final: 0.8585 (mtpp) REVERT: F 74 GLU cc_start: 0.8014 (tt0) cc_final: 0.7666 (mt-10) REVERT: G 110 ASN cc_start: 0.8616 (p0) cc_final: 0.8353 (p0) REVERT: H 32 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7610 (mt-10) outliers start: 14 outliers final: 6 residues processed: 106 average time/residue: 1.8866 time to fit residues: 210.5671 Evaluate side-chains 105 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.180959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142351 restraints weight = 11378.347| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 0.79 r_work: 0.3385 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11875 Z= 0.154 Angle : 0.525 6.950 17126 Z= 0.321 Chirality : 0.033 0.123 1954 Planarity : 0.003 0.033 1289 Dihedral : 29.343 162.784 3623 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.76 % Allowed : 12.96 % 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 (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: 2.75 (0.31), residues: 735 helix: 2.80 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.02 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 75 PHE 0.007 0.001 PHE F 61 TYR 0.007 0.001 TYR F 51 ARG 0.006 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04921 ( 709) hydrogen bonds : angle 2.59832 ( 1795) covalent geometry : bond 0.00322 (11875) covalent geometry : angle 0.52504 (17126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.828 Fit side-chains REVERT: D 43 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7831 (mmmt) REVERT: D 116 THR cc_start: 0.8034 (t) cc_final: 0.7822 (m) REVERT: E 50 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: F 44 LYS cc_start: 0.8843 (tttm) cc_final: 0.8611 (ttmm) REVERT: H 32 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7911 (mt-10) outliers start: 11 outliers final: 5 residues processed: 109 average time/residue: 1.7871 time to fit residues: 205.4583 Evaluate side-chains 110 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain H residue 32 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 18 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.177947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138180 restraints weight = 11312.749| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 0.80 r_work: 0.3311 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11875 Z= 0.191 Angle : 0.556 7.804 17126 Z= 0.336 Chirality : 0.035 0.129 1954 Planarity : 0.004 0.032 1289 Dihedral : 29.436 162.820 3623 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.76 % Allowed : 14.08 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.67 (0.31), residues: 735 helix: 2.75 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.06 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.013 0.002 PHE A 78 TYR 0.011 0.001 TYR F 51 ARG 0.008 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.06055 ( 709) hydrogen bonds : angle 2.67555 ( 1795) covalent geometry : bond 0.00423 (11875) covalent geometry : angle 0.55580 (17126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.817 Fit side-chains REVERT: B 77 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8554 (mtpt) REVERT: D 43 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7753 (mmmt) REVERT: D 116 THR cc_start: 0.8168 (t) cc_final: 0.7954 (m) REVERT: E 50 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: F 44 LYS cc_start: 0.8857 (tttm) cc_final: 0.8635 (ttmm) REVERT: H 32 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7605 (mt-10) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 1.8181 time to fit residues: 207.1462 Evaluate side-chains 112 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.178161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.139071 restraints weight = 11245.856| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 0.77 r_work: 0.3340 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11875 Z= 0.171 Angle : 0.548 7.629 17126 Z= 0.332 Chirality : 0.034 0.128 1954 Planarity : 0.004 0.032 1289 Dihedral : 29.434 162.785 3623 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.92 % Allowed : 13.60 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.67 (0.31), residues: 735 helix: 2.75 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.07 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.011 0.002 PHE A 78 TYR 0.011 0.001 TYR F 51 ARG 0.007 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.05927 ( 709) hydrogen bonds : angle 2.68401 ( 1795) covalent geometry : bond 0.00367 (11875) covalent geometry : angle 0.54795 (17126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.802 Fit side-chains REVERT: B 77 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8541 (mtpt) REVERT: D 43 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7800 (mmmt) REVERT: D 116 THR cc_start: 0.8144 (t) cc_final: 0.7940 (m) REVERT: E 50 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: F 44 LYS cc_start: 0.8847 (tttm) cc_final: 0.8622 (ttmm) REVERT: H 32 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7617 (mt-10) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 1.8711 time to fit residues: 207.0874 Evaluate side-chains 113 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.178251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.138237 restraints weight = 11300.347| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 0.81 r_work: 0.3331 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11875 Z= 0.172 Angle : 0.548 7.902 17126 Z= 0.332 Chirality : 0.034 0.127 1954 Planarity : 0.004 0.032 1289 Dihedral : 29.433 162.775 3623 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.92 % Allowed : 13.76 % Favored : 84.32 % 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: 2.70 (0.31), residues: 735 helix: 2.77 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.06 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.010 0.002 PHE A 78 TYR 0.010 0.001 TYR F 51 ARG 0.006 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.05846 ( 709) hydrogen bonds : angle 2.69129 ( 1795) covalent geometry : bond 0.00371 (11875) covalent geometry : angle 0.54784 (17126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.828 Fit side-chains REVERT: B 77 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8540 (mtpt) REVERT: D 43 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7783 (mmmt) REVERT: D 116 THR cc_start: 0.8146 (t) cc_final: 0.7940 (m) REVERT: E 50 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: F 44 LYS cc_start: 0.8849 (tttm) cc_final: 0.8621 (ttmm) REVERT: H 32 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7580 (mt-10) outliers start: 12 outliers final: 10 residues processed: 105 average time/residue: 2.0766 time to fit residues: 229.7372 Evaluate side-chains 114 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.178685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139148 restraints weight = 11186.657| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 0.80 r_work: 0.3331 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11875 Z= 0.156 Angle : 0.540 7.310 17126 Z= 0.328 Chirality : 0.033 0.126 1954 Planarity : 0.004 0.032 1289 Dihedral : 29.428 162.880 3623 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.76 % Allowed : 14.08 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.73 (0.31), residues: 735 helix: 2.79 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.05 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 75 PHE 0.010 0.001 PHE A 78 TYR 0.011 0.001 TYR F 51 ARG 0.006 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.05730 ( 709) hydrogen bonds : angle 2.68438 ( 1795) covalent geometry : bond 0.00322 (11875) covalent geometry : angle 0.53975 (17126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7728.68 seconds wall clock time: 133 minutes 25.67 seconds (8005.67 seconds total)