Starting phenix.real_space_refine on Thu Jul 2 21:41:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8com_16777/07_2026/8com_16777.cif Found real_map, /net/cci-nas-00/data/ceres_data/8com_16777/07_2026/8com_16777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8com_16777/07_2026/8com_16777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8com_16777/07_2026/8com_16777.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8com_16777/07_2026/8com_16777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8com_16777/07_2026/8com_16777.map" } resolution = 3.3 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= 0.001 sd= 0.076 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 254 5.49 5 S 18 5.16 5 C 5887 2.51 5 N 2043 2.21 5 O 2503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10705 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "B" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 597 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain: "C" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 732 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "E" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 669 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "F" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 592 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "G" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 736 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "I" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2620 Classifications: {'DNA': 127} Link IDs: {'rna3p': 126} Chain: "J" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2587 Classifications: {'DNA': 127} Link IDs: {'rna3p': 126} Time building chain proxies: 2.05, per 1000 atoms: 0.19 Number of scatterers: 10705 At special positions: 0 Unit cell: (73.781, 116.06, 115.231, 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 18 16.00 P 254 15.00 O 2503 8.00 N 2043 7.00 C 5887 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: 1.06 Conformation dependent library (CDL) restraints added in 230.5 milliseconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 74.6% alpha, 2.5% beta 126 base pairs and 210 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.648A pdb=" N ARG A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.589A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 111 removed outlier: 3.651A pdb=" N LEU A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'B' and resid 28 through 40 Processing helix chain 'B' and resid 47 through 74 removed outlier: 3.639A pdb=" N GLU B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 44 through 72 removed outlier: 3.629A pdb=" N ALA C 48 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 93 through 99 Processing helix chain 'D' and resid 25 through 37 removed outlier: 3.624A pdb=" N ILE D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 73 Processing helix chain 'D' and resid 78 through 90 Processing helix chain 'D' and resid 91 through 111 removed outlier: 3.846A pdb=" N HIS D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 92 through 111 removed outlier: 3.540A pdb=" N TYR E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 47 through 74 removed outlier: 3.734A pdb=" N GLU F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 Processing helix chain 'G' and resid 15 through 20 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 44 through 73 removed outlier: 3.603A pdb=" N ALA G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 Processing helix chain 'G' and resid 94 through 99 Processing helix chain 'H' and resid 25 through 37 Processing helix chain 'H' and resid 43 through 72 Processing helix chain 'H' and resid 79 through 90 Processing helix chain 'H' and resid 91 through 111 removed outlier: 3.680A pdb=" N HIS H 97 " --> pdb=" O ASP H 93 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 111 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.234A pdb=" N ARG A 80 " --> pdb=" O VAL B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=AA3, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 104 removed outlier: 6.823A pdb=" N THR C 103 " --> pdb=" O TYR F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 80 through 81 removed outlier: 8.289A pdb=" N ARG E 80 " --> pdb=" O VAL F 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.410A pdb=" N ARG G 42 " --> pdb=" O LEU H 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 79 through 80 385 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 327 hydrogen bonds 654 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 210 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2175 1.33 - 1.45: 3568 1.45 - 1.57: 5110 1.57 - 1.69: 506 1.69 - 1.81: 32 Bond restraints: 11391 Sorted by residual: bond pdb=" C3' DG I -21 " pdb=" C2' DG I -21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DC I 7 " pdb=" C2' DC I 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DC I -58 " pdb=" C2' DC I -58 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.87e+00 bond pdb=" C3' DG I 21 " pdb=" C2' DG I 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.71e+00 bond pdb=" C3' DC I 30 " pdb=" C2' DC I 30 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.25e+00 ... (remaining 11386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 15758 1.80 - 3.60: 679 3.60 - 5.40: 23 5.40 - 7.20: 3 7.20 - 8.99: 2 Bond angle restraints: 16465 Sorted by residual: angle pdb=" N VAL C 27 " pdb=" CA VAL C 27 " pdb=" C VAL C 27 " ideal model delta sigma weight residual 113.47 108.61 4.86 1.01e+00 9.80e-01 2.31e+01 angle pdb=" N3 DT I 13 " pdb=" C4 DT I 13 " pdb=" O4 DT I 13 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I 15 " pdb=" C4 DT I 15 " pdb=" O4 DT I 15 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.05e+01 angle pdb=" O4' DT J 15 " pdb=" C1' DT J 15 " pdb=" N1 DT J 15 " ideal model delta sigma weight residual 108.00 111.12 -3.12 7.00e-01 2.04e+00 1.99e+01 angle pdb=" N3 DT I -57 " pdb=" C4 DT I -57 " pdb=" O4 DT I -57 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 ... (remaining 16460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.04: 4650 30.04 - 60.09: 1493 60.09 - 90.13: 40 90.13 - 120.18: 1 120.18 - 150.22: 4 Dihedral angle restraints: 6188 sinusoidal: 4152 harmonic: 2036 Sorted by residual: dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DT I -16 " ideal model delta sinusoidal sigma weight residual 220.00 69.78 150.22 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC J 4 " pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " pdb=" P DC J 5 " ideal model delta sinusoidal sigma weight residual 220.00 75.92 144.08 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DG I -21 " pdb=" C3' DG I -21 " pdb=" O3' DG I -21 " pdb=" P DC I -20 " ideal model delta sinusoidal sigma weight residual 220.00 94.78 125.22 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 6185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 982 0.029 - 0.058: 595 0.058 - 0.087: 220 0.087 - 0.116: 89 0.116 - 0.145: 14 Chirality restraints: 1900 Sorted by residual: chirality pdb=" C3' DC I -58 " pdb=" C4' DC I -58 " pdb=" O3' DC I -58 " pdb=" C2' DC I -58 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CG LEU E 127 " pdb=" CB LEU E 127 " pdb=" CD1 LEU E 127 " pdb=" CD2 LEU E 127 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" C3' DG I -21 " pdb=" C4' DG I -21 " pdb=" O3' DG I -21 " pdb=" C2' DG I -21 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1897 not shown) Planarity restraints: 1198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 20 " 0.023 2.00e-02 2.50e+03 1.11e-02 3.70e+00 pdb=" N9 DG I 20 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DG I 20 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 20 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 20 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 20 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG I 20 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DG I 20 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 20 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 20 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG I 20 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 20 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 28 " 0.012 2.00e-02 2.50e+03 1.23e-02 3.05e+00 pdb=" CG TYR H 28 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR H 28 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR H 28 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR H 28 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR H 28 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR H 28 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 28 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -4 " 0.021 2.00e-02 2.50e+03 8.79e-03 2.32e+00 pdb=" N9 DG I -4 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG I -4 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I -4 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG I -4 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -4 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I -4 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I -4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -4 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I -4 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I -4 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I -4 " -0.002 2.00e-02 2.50e+03 ... (remaining 1195 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1639 2.76 - 3.30: 9909 3.30 - 3.83: 21739 3.83 - 4.37: 24091 4.37 - 4.90: 35191 Nonbonded interactions: 92569 Sorted by model distance: nonbonded pdb=" OE1 GLU E 91 " pdb=" OH TYR F 98 " model vdw 2.228 3.040 nonbonded pdb=" OG SER E 54 " pdb=" OD1 ASP E 56 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR B 73 " pdb=" OE2 GLU D 81 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP D 56 " pdb=" OH TYR F 96 " model vdw 2.291 3.040 nonbonded pdb=" N LYS E 61 " pdb=" OP1 DG I 18 " model vdw 2.308 3.120 ... (remaining 92564 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 45 through 129) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 98) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 111) } 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 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: 2.170 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.110 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 0.036 11391 Z= 0.512 Angle : 0.738 8.994 16465 Z= 0.655 Chirality : 0.043 0.145 1900 Planarity : 0.003 0.029 1198 Dihedral : 28.543 150.219 4872 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.34 % Allowed : 13.97 % Favored : 85.69 % 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: 2.02 (0.32), residues: 692 helix: 2.12 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -0.96 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.030 0.002 TYR H 28 PHE 0.011 0.002 PHE H 58 TRP 0.007 0.001 TRP H 25 HIS 0.001 0.000 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.51 (11391) covalent geometry : angle 0.73849 / 0.66 (16465) hydrogen bonds : bond 0.12100 / 8.10 ( 712) hydrogen bonds : angle 4.06014 / 3.09 ( 1809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.254 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.1033 time to fit residues: 11.7143 Evaluate side-chains 81 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain E residue 94 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.173990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125246 restraints weight = 14514.716| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.85 r_work: 0.3400 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11391 Z= 0.151 Angle : 0.624 7.379 16465 Z= 0.373 Chirality : 0.043 0.206 1900 Planarity : 0.003 0.038 1198 Dihedral : 31.436 154.517 3557 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.07 % Allowed : 12.41 % Favored : 85.52 % 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: 2.05 (0.32), residues: 692 helix: 2.10 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.07 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.022 0.002 TYR H 28 PHE 0.012 0.002 PHE A 64 TRP 0.008 0.002 TRP D 25 HIS 0.001 0.000 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.15 (11391) covalent geometry : angle 0.62444 / 0.37 (16465) hydrogen bonds : bond 0.04983 / 3.48 ( 712) hydrogen bonds : angle 3.05492 / 2.28 ( 1809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.276 Fit side-chains REVERT: B 75 ARG cc_start: 0.8903 (mmt-90) cc_final: 0.8557 (mmt90) REVERT: D 72 ASN cc_start: 0.8724 (m-40) cc_final: 0.8452 (m-40) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.1047 time to fit residues: 13.0943 Evaluate side-chains 84 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.173324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124494 restraints weight = 14751.023| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.90 r_work: 0.3389 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11391 Z= 0.153 Angle : 0.613 8.575 16465 Z= 0.362 Chirality : 0.042 0.215 1900 Planarity : 0.003 0.038 1198 Dihedral : 31.527 153.932 3554 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.76 % Allowed : 12.41 % Favored : 84.83 % 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: 2.15 (0.32), residues: 692 helix: 2.19 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.13 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 17 TYR 0.018 0.002 TYR H 28 PHE 0.012 0.002 PHE A 64 TRP 0.007 0.001 TRP D 25 HIS 0.001 0.000 HIS E 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (11391) covalent geometry : angle 0.61332 / 0.36 (16465) hydrogen bonds : bond 0.04632 / 3.24 ( 712) hydrogen bonds : angle 2.87574 / 2.14 ( 1809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.221 Fit side-chains REVERT: A 76 LYS cc_start: 0.6773 (tmtt) cc_final: 0.6152 (tmtt) REVERT: D 72 ASN cc_start: 0.8701 (m-40) cc_final: 0.8433 (m-40) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 0.0919 time to fit residues: 12.6303 Evaluate side-chains 92 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.173544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124934 restraints weight = 14959.471| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.91 r_work: 0.3391 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11391 Z= 0.147 Angle : 0.604 7.709 16465 Z= 0.355 Chirality : 0.041 0.222 1900 Planarity : 0.003 0.035 1198 Dihedral : 31.520 154.625 3551 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.93 % Allowed : 13.79 % Favored : 83.28 % 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: 2.24 (0.32), residues: 692 helix: 2.26 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.13 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.016 0.002 TYR H 28 PHE 0.012 0.002 PHE A 64 TRP 0.008 0.001 TRP D 25 HIS 0.001 0.000 HIS E 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (11391) covalent geometry : angle 0.60419 / 0.36 (16465) hydrogen bonds : bond 0.04417 / 3.11 ( 712) hydrogen bonds : angle 2.78275 / 2.07 ( 1809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.258 Fit side-chains REVERT: A 76 LYS cc_start: 0.6823 (tmtt) cc_final: 0.6229 (tmtt) REVERT: D 56 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8273 (p0) REVERT: D 72 ASN cc_start: 0.8694 (m-40) cc_final: 0.8425 (m-40) outliers start: 17 outliers final: 13 residues processed: 95 average time/residue: 0.1032 time to fit residues: 13.5270 Evaluate side-chains 96 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 7 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.174396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125695 restraints weight = 14831.316| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.91 r_work: 0.3403 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11391 Z= 0.137 Angle : 0.592 7.954 16465 Z= 0.350 Chirality : 0.041 0.236 1900 Planarity : 0.003 0.035 1198 Dihedral : 31.486 154.663 3551 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.10 % Allowed : 14.14 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.29 (0.32), residues: 692 helix: 2.30 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.13 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 45 TYR 0.015 0.002 TYR H 28 PHE 0.013 0.002 PHE A 64 TRP 0.007 0.001 TRP D 25 HIS 0.001 0.000 HIS E 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (11391) covalent geometry : angle 0.59213 / 0.35 (16465) hydrogen bonds : bond 0.04253 / 3.00 ( 712) hydrogen bonds : angle 2.71767 / 2.03 ( 1809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.259 Fit side-chains REVERT: A 76 LYS cc_start: 0.6854 (tmtt) cc_final: 0.6267 (tmtt) REVERT: B 75 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8503 (mmt90) REVERT: D 72 ASN cc_start: 0.8709 (m-40) cc_final: 0.8494 (m110) outliers start: 18 outliers final: 14 residues processed: 95 average time/residue: 0.1069 time to fit residues: 14.3328 Evaluate side-chains 94 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 71 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 40.0000 chunk 89 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.168778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119506 restraints weight = 14655.680| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.89 r_work: 0.3334 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11391 Z= 0.233 Angle : 0.686 7.847 16465 Z= 0.385 Chirality : 0.045 0.228 1900 Planarity : 0.004 0.036 1198 Dihedral : 31.752 155.699 3551 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.83 % Allowed : 15.00 % Favored : 80.17 % 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: 1.73 (0.31), residues: 692 helix: 1.90 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.36 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 45 TYR 0.015 0.002 TYR G 57 PHE 0.011 0.002 PHE A 64 TRP 0.008 0.002 TRP H 25 HIS 0.002 0.001 HIS E 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (11391) covalent geometry : angle 0.68646 / 0.39 (16465) hydrogen bonds : bond 0.05118 / 3.59 ( 712) hydrogen bonds : angle 3.14474 / 2.32 ( 1809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6824 (mtt-85) REVERT: B 75 ARG cc_start: 0.8921 (mmt-90) cc_final: 0.8624 (mmt90) REVERT: C 76 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7477 (pttm) REVERT: D 56 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8323 (p0) outliers start: 28 outliers final: 22 residues processed: 103 average time/residue: 0.1122 time to fit residues: 15.9985 Evaluate side-chains 110 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 81 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.172802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123890 restraints weight = 14910.565| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.92 r_work: 0.3380 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11391 Z= 0.137 Angle : 0.598 8.882 16465 Z= 0.351 Chirality : 0.041 0.250 1900 Planarity : 0.003 0.037 1198 Dihedral : 31.502 158.603 3551 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.76 % Allowed : 16.90 % Favored : 80.34 % 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: 2.11 (0.32), residues: 692 helix: 2.19 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.26 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 45 TYR 0.017 0.002 TYR H 28 PHE 0.015 0.002 PHE A 64 TRP 0.009 0.001 TRP D 25 HIS 0.001 0.000 HIS E 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (11391) covalent geometry : angle 0.59820 / 0.35 (16465) hydrogen bonds : bond 0.04226 / 2.97 ( 712) hydrogen bonds : angle 2.79121 / 2.07 ( 1809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.288 Fit side-chains REVERT: B 75 ARG cc_start: 0.8847 (mmt-90) cc_final: 0.8572 (mmt90) REVERT: F 66 ASP cc_start: 0.8048 (m-30) cc_final: 0.7186 (m-30) outliers start: 16 outliers final: 12 residues processed: 90 average time/residue: 0.1064 time to fit residues: 13.5940 Evaluate side-chains 92 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.173091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124195 restraints weight = 14921.397| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.92 r_work: 0.3383 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11391 Z= 0.135 Angle : 0.597 8.037 16465 Z= 0.350 Chirality : 0.041 0.249 1900 Planarity : 0.003 0.037 1198 Dihedral : 31.490 164.605 3551 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.76 % Allowed : 17.41 % Favored : 79.83 % 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: 2.14 (0.32), residues: 692 helix: 2.22 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.27 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.016 0.002 TYR H 28 PHE 0.014 0.002 PHE A 64 TRP 0.008 0.001 TRP D 25 HIS 0.001 0.000 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (11391) covalent geometry : angle 0.59746 / 0.35 (16465) hydrogen bonds : bond 0.04198 / 2.96 ( 712) hydrogen bonds : angle 2.76520 / 2.05 ( 1809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.320 Fit side-chains REVERT: A 76 LYS cc_start: 0.6822 (tmtt) cc_final: 0.6268 (tmtt) REVERT: B 75 ARG cc_start: 0.8852 (mmt-90) cc_final: 0.8589 (mmt90) outliers start: 16 outliers final: 13 residues processed: 92 average time/residue: 0.1152 time to fit residues: 14.7674 Evaluate side-chains 95 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 74 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.171616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122577 restraints weight = 14656.100| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.87 r_work: 0.3371 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11391 Z= 0.172 Angle : 0.621 8.713 16465 Z= 0.358 Chirality : 0.041 0.245 1900 Planarity : 0.004 0.043 1198 Dihedral : 31.520 168.404 3551 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.59 % Allowed : 17.93 % Favored : 79.48 % 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: 2.09 (0.32), residues: 692 helix: 2.19 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.33 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.014 0.002 TYR G 50 PHE 0.012 0.002 PHE H 58 TRP 0.007 0.001 TRP D 25 HIS 0.002 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (11391) covalent geometry : angle 0.62066 / 0.36 (16465) hydrogen bonds : bond 0.04322 / 3.04 ( 712) hydrogen bonds : angle 2.84201 / 2.10 ( 1809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.220 Fit side-chains REVERT: A 76 LYS cc_start: 0.6959 (tmtt) cc_final: 0.6397 (tmtt) REVERT: B 75 ARG cc_start: 0.8845 (mmt-90) cc_final: 0.8575 (mmt90) REVERT: D 56 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8284 (p0) outliers start: 15 outliers final: 14 residues processed: 89 average time/residue: 0.1099 time to fit residues: 13.4279 Evaluate side-chains 97 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 36 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 chunk 17 optimal weight: 0.0020 chunk 73 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 0.0270 chunk 80 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.4446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.174891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.126312 restraints weight = 14847.916| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.92 r_work: 0.3411 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11391 Z= 0.125 Angle : 0.581 8.387 16465 Z= 0.344 Chirality : 0.040 0.257 1900 Planarity : 0.003 0.036 1198 Dihedral : 31.381 174.915 3551 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.24 % Allowed : 18.45 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.31 (0.32), residues: 692 helix: 2.34 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.23 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.013 0.002 TYR H 28 PHE 0.015 0.002 PHE A 64 TRP 0.011 0.002 TRP D 25 HIS 0.001 0.000 HIS H 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.12 (11391) covalent geometry : angle 0.58051 / 0.34 (16465) hydrogen bonds : bond 0.04043 / 2.86 ( 712) hydrogen bonds : angle 2.65789 / 1.97 ( 1809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.275 Fit side-chains REVERT: A 76 LYS cc_start: 0.6865 (tmtt) cc_final: 0.6304 (tmtt) REVERT: B 75 ARG cc_start: 0.8792 (mmt-90) cc_final: 0.8537 (mmt90) REVERT: D 56 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8193 (p0) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 0.1184 time to fit residues: 15.2785 Evaluate side-chains 92 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 78 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 40.0000 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.170791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121639 restraints weight = 14872.616| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.91 r_work: 0.3358 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11391 Z= 0.179 Angle : 0.636 8.539 16465 Z= 0.362 Chirality : 0.042 0.247 1900 Planarity : 0.004 0.036 1198 Dihedral : 31.574 175.811 3551 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.28 % Allowed : 17.76 % Favored : 78.97 % 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: 2.05 (0.32), residues: 692 helix: 2.16 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.36 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.015 0.002 TYR G 57 PHE 0.011 0.002 PHE A 64 TRP 0.005 0.002 TRP H 25 HIS 0.002 0.000 HIS E 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (11391) covalent geometry : angle 0.63556 / 0.36 (16465) hydrogen bonds : bond 0.04565 / 3.20 ( 712) hydrogen bonds : angle 2.92020 / 2.15 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2061.24 seconds wall clock time: 36 minutes 2.25 seconds (2162.25 seconds total)