Starting phenix.real_space_refine on Wed Aug 5 15:22:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8com_16777/08_2026/8com_16777.cif Found real_map, /net/cci-nas-00/data/ceres_data/8com_16777/08_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_16777/08_2026/8com_16777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8com_16777/08_2026/8com_16777.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8com_16777/08_2026/8com_16777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8com_16777/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 2.01, 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: 0.91 Conformation dependent library (CDL) restraints added in 219.2 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: 1.46 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: 1.92 Time building geometry restraints manager: 1.22 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: 15747 1.80 - 3.60: 690 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: 2.800 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.330 Find NCS groups from input model: 0.200 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.440 ------------------------------------------------------------------------------- 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 : 0.746 8.994 16465 Z= 0.662 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 0.74632 / 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 : 0.238 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.0904 time to fit residues: 10.3672 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 : 0.177 ------------------------------------------------------------------------------- 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 = 0.174015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125431 restraints weight = 14509.767| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.85 r_work: 0.3404 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11391 Z= 0.150 Angle : 0.642 7.672 16465 Z= 0.376 Chirality : 0.043 0.221 1900 Planarity : 0.003 0.038 1198 Dihedral : 31.385 153.843 3557 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.24 % Allowed : 12.41 % Favored : 85.34 % 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: 2.02 (0.32), residues: 692 helix: 2.09 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.13 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.023 0.002 TYR H 28 PHE 0.012 0.002 PHE A 64 TRP 0.009 0.002 TRP D 25 HIS 0.001 0.000 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.15 (11391) covalent geometry : angle 0.64155 / 0.38 (16465) hydrogen bonds : bond 0.04927 / 3.45 ( 712) hydrogen bonds : angle 3.04595 / 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 95 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.219 Fit side-chains REVERT: B 75 ARG cc_start: 0.8919 (mmt-90) cc_final: 0.8553 (mmt90) REVERT: D 72 ASN cc_start: 0.8709 (m-40) cc_final: 0.8441 (m-40) outliers start: 13 outliers final: 10 residues processed: 89 average time/residue: 0.0991 time to fit residues: 12.4966 Evaluate side-chains 86 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 53 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 9 optimal weight: 0.0010 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.174650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126095 restraints weight = 14763.238| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.91 r_work: 0.3409 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.0889 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 : 0.616 8.591 16465 Z= 0.361 Chirality : 0.042 0.241 1900 Planarity : 0.003 0.039 1198 Dihedral : 31.384 152.646 3554 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.07 % Allowed : 13.45 % 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 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: 2.25 (0.32), residues: 692 helix: 2.27 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.10 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 17 TYR 0.018 0.002 TYR F 73 PHE 0.013 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 0.00219 / 0.14 (11391) covalent geometry : angle 0.61638 / 0.36 (16465) hydrogen bonds : bond 0.04486 / 3.14 ( 712) hydrogen bonds : angle 2.79780 / 2.09 ( 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 95 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.205 Fit side-chains REVERT: A 76 LYS cc_start: 0.6795 (tmtt) cc_final: 0.6171 (tmtt) REVERT: D 72 ASN cc_start: 0.8678 (m-40) cc_final: 0.8402 (m-40) REVERT: F 90 LYS cc_start: 0.8275 (tmtt) cc_final: 0.8042 (tmtt) outliers start: 12 outliers final: 7 residues processed: 91 average time/residue: 0.0872 time to fit residues: 11.4768 Evaluate side-chains 85 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 72 SER 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: 0.8980 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.174273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125594 restraints weight = 14951.533| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.91 r_work: 0.3402 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1157 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= 0.142 Angle : 0.618 7.840 16465 Z= 0.357 Chirality : 0.042 0.241 1900 Planarity : 0.003 0.037 1198 Dihedral : 31.419 153.221 3551 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.10 % Allowed : 13.79 % Favored : 83.10 % 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: 2.28 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.04 (0.46), residues: 167 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 A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (11391) covalent geometry : angle 0.61754 / 0.36 (16465) hydrogen bonds : bond 0.04374 / 3.08 ( 712) hydrogen bonds : angle 2.75983 / 2.06 ( 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 102 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.262 Fit side-chains REVERT: A 76 LYS cc_start: 0.6813 (tmtt) cc_final: 0.6200 (tmtt) REVERT: D 56 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8281 (p0) REVERT: D 72 ASN cc_start: 0.8721 (m-40) cc_final: 0.8438 (m-40) REVERT: F 66 ASP cc_start: 0.8307 (m-30) cc_final: 0.8034 (m-30) REVERT: F 90 LYS cc_start: 0.8293 (tmtt) cc_final: 0.7995 (tmtt) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 0.1003 time to fit residues: 13.2521 Evaluate side-chains 96 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 71 VAL 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: 0.8980 chunk 54 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 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 = 0.4160 r_free = 0.4160 target = 0.175475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126687 restraints weight = 14865.671| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.92 r_work: 0.3415 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11391 Z= 0.133 Angle : 0.598 8.183 16465 Z= 0.349 Chirality : 0.041 0.262 1900 Planarity : 0.004 0.063 1198 Dihedral : 31.333 153.384 3551 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.93 % Allowed : 14.31 % 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: 2.41 (0.32), residues: 692 helix: 2.38 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.04 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 45 TYR 0.017 0.002 TYR H 28 PHE 0.014 0.002 PHE E 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 0.00221 / 0.13 (11391) covalent geometry : angle 0.59844 / 0.35 (16465) hydrogen bonds : bond 0.04167 / 2.94 ( 712) hydrogen bonds : angle 2.65817 / 1.98 ( 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 102 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.200 Fit side-chains REVERT: A 46 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6745 (mtt-85) REVERT: A 76 LYS cc_start: 0.6841 (tmtt) cc_final: 0.6262 (tmtt) REVERT: C 76 LYS cc_start: 0.8112 (mmtm) cc_final: 0.7335 (pttm) REVERT: F 90 LYS cc_start: 0.8289 (tmtt) cc_final: 0.8081 (tmtt) outliers start: 17 outliers final: 12 residues processed: 94 average time/residue: 0.0914 time to fit residues: 11.8594 Evaluate side-chains 93 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG 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 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 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: 4.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.169651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120531 restraints weight = 14616.391| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.84 r_work: 0.3343 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11391 Z= 0.219 Angle : 0.688 7.879 16465 Z= 0.382 Chirality : 0.045 0.249 1900 Planarity : 0.004 0.035 1198 Dihedral : 31.586 154.116 3551 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.66 % Allowed : 13.97 % Favored : 81.38 % 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: 1.86 (0.32), residues: 692 helix: 1.99 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.30 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 45 TYR 0.015 0.002 TYR G 50 PHE 0.011 0.002 PHE A 64 TRP 0.007 0.002 TRP H 25 HIS 0.002 0.001 HIS E 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (11391) covalent geometry : angle 0.68821 / 0.38 (16465) hydrogen bonds : bond 0.04992 / 3.50 ( 712) hydrogen bonds : angle 3.05769 / 2.26 ( 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 114 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6854 (mtt-85) REVERT: B 75 ARG cc_start: 0.8890 (mmt-90) cc_final: 0.8577 (mmt90) REVERT: D 56 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8348 (p0) REVERT: F 66 ASP cc_start: 0.8521 (m-30) cc_final: 0.8234 (m-30) REVERT: F 70 TYR cc_start: 0.8426 (m-80) cc_final: 0.8224 (m-80) outliers start: 27 outliers final: 21 residues processed: 101 average time/residue: 0.1019 time to fit residues: 14.4208 Evaluate side-chains 107 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 81 THR 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 48 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 71 THR 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: 3.9990 chunk 81 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 71 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.173624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125010 restraints weight = 14903.326| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.92 r_work: 0.3392 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11391 Z= 0.131 Angle : 0.606 8.683 16465 Z= 0.352 Chirality : 0.042 0.270 1900 Planarity : 0.003 0.036 1198 Dihedral : 31.327 155.319 3551 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.59 % Allowed : 16.21 % Favored : 81.21 % 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: 2.22 (0.32), residues: 692 helix: 2.25 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.16 (0.46), 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 0.014 0.002 PHE A 64 TRP 0.008 0.001 TRP D 25 HIS 0.001 0.000 HIS E 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 (11391) covalent geometry : angle 0.60638 / 0.35 (16465) hydrogen bonds : bond 0.04183 / 2.95 ( 712) hydrogen bonds : angle 2.73940 / 2.04 ( 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 98 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.271 Fit side-chains REVERT: B 75 ARG cc_start: 0.8813 (mmt-90) cc_final: 0.8521 (mmt90) REVERT: C 76 LYS cc_start: 0.8142 (mmtm) cc_final: 0.7422 (pttm) outliers start: 15 outliers final: 13 residues processed: 91 average time/residue: 0.0982 time to fit residues: 12.7518 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 : 0.193 ------------------------------------------------------------------------------- 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 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 38 SER 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: 0.9990 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 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 = 0.4138 r_free = 0.4138 target = 0.173611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124845 restraints weight = 14939.195| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.92 r_work: 0.3392 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1671 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= 0.133 Angle : 0.608 7.982 16465 Z= 0.352 Chirality : 0.041 0.268 1900 Planarity : 0.003 0.036 1198 Dihedral : 31.318 159.824 3551 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.59 % Allowed : 17.59 % 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: 2.26 (0.32), residues: 692 helix: 2.28 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.15 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 19 TYR 0.015 0.002 TYR H 28 PHE 0.014 0.002 PHE A 64 TRP 0.007 0.001 TRP D 25 HIS 0.001 0.000 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (11391) covalent geometry : angle 0.60799 / 0.35 (16465) hydrogen bonds : bond 0.04168 / 2.94 ( 712) hydrogen bonds : angle 2.72428 / 2.02 ( 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 97 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.153 Fit side-chains REVERT: A 76 LYS cc_start: 0.6802 (tmtt) cc_final: 0.6240 (tmtt) REVERT: B 75 ARG cc_start: 0.8817 (mmt-90) cc_final: 0.8524 (mmt90) REVERT: C 76 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7412 (pttm) outliers start: 15 outliers final: 12 residues processed: 91 average time/residue: 0.1020 time to fit residues: 12.8813 Evaluate side-chains 93 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 81 THR Chi-restraints excluded: chain D residue 42 MET 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: 0.0370 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: 0.6980 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.174238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125606 restraints weight = 14979.505| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.92 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: 0.1733 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= 0.129 Angle : 0.601 8.066 16465 Z= 0.349 Chirality : 0.041 0.272 1900 Planarity : 0.004 0.071 1198 Dihedral : 31.295 168.232 3551 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.24 % Allowed : 18.10 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.32), residues: 692 helix: 2.31 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.14 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.015 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 E 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.13 (11391) covalent geometry : angle 0.60073 / 0.35 (16465) hydrogen bonds : bond 0.04117 / 2.90 ( 712) hydrogen bonds : angle 2.69076 / 1.99 ( 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 93 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.263 Fit side-chains REVERT: A 76 LYS cc_start: 0.6964 (tmtt) cc_final: 0.6397 (tmtt) REVERT: B 75 ARG cc_start: 0.8827 (mmt-90) cc_final: 0.8544 (mmt90) REVERT: D 56 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8232 (p0) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 0.0914 time to fit residues: 11.1682 Evaluate side-chains 91 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 81 THR Chi-restraints excluded: chain D residue 42 MET 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 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 36 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 17 optimal weight: 0.0980 chunk 73 optimal weight: 20.0000 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 80 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.175836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127113 restraints weight = 14603.012| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.88 r_work: 0.3432 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1908 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= 0.123 Angle : 0.586 7.853 16465 Z= 0.343 Chirality : 0.040 0.274 1900 Planarity : 0.003 0.036 1198 Dihedral : 31.235 176.825 3551 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.90 % Allowed : 18.28 % 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: 2.51 (0.32), residues: 692 helix: 2.48 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.16 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 19 TYR 0.014 0.002 TYR H 28 PHE 0.013 0.001 PHE A 64 TRP 0.009 0.002 TRP D 25 HIS 0.001 0.000 HIS E 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.12 (11391) covalent geometry : angle 0.58607 / 0.34 (16465) hydrogen bonds : bond 0.04010 / 2.84 ( 712) hydrogen bonds : angle 2.60265 / 1.93 ( 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 95 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.153 Fit side-chains REVERT: A 76 LYS cc_start: 0.6853 (tmtt) cc_final: 0.6307 (tmtt) REVERT: B 75 ARG cc_start: 0.8798 (mmt-90) cc_final: 0.8524 (mmt90) outliers start: 11 outliers final: 9 residues processed: 90 average time/residue: 0.1005 time to fit residues: 12.4389 Evaluate side-chains 91 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 35 optimal weight: 3.9990 chunk 79 optimal weight: 40.0000 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.173058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124199 restraints weight = 14926.969| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.92 r_work: 0.3390 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11391 Z= 0.155 Angle : 0.623 8.624 16465 Z= 0.353 Chirality : 0.042 0.270 1900 Planarity : 0.003 0.035 1198 Dihedral : 31.360 175.870 3551 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.72 % Allowed : 18.79 % 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: 2.41 (0.32), residues: 692 helix: 2.42 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.21 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.016 0.002 TYR F 73 PHE 0.012 0.002 PHE H 58 TRP 0.005 0.001 TRP D 25 HIS 0.001 0.000 HIS E 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (11391) covalent geometry : angle 0.62290 / 0.35 (16465) hydrogen bonds : bond 0.04287 / 3.02 ( 712) hydrogen bonds : angle 2.75992 / 2.04 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.33 seconds wall clock time: 32 minutes 47.69 seconds (1967.69 seconds total)