Starting phenix.real_space_refine on Fri Jul 3 00:08:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nl0_12453/07_2026/7nl0_12453.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nl0_12453/07_2026/7nl0_12453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nl0_12453/07_2026/7nl0_12453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nl0_12453/07_2026/7nl0_12453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nl0_12453/07_2026/7nl0_12453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nl0_12453/07_2026/7nl0_12453.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 262 5.49 5 S 14 5.16 5 C 6334 2.51 5 N 2121 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s 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: 11363 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2715 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2656 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Time building chain proxies: 2.33, per 1000 atoms: 0.21 Number of scatterers: 11363 At special positions: 0 Unit cell: (75.9676, 120.12, 116.873, 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 14 16.00 P 262 15.00 O 2632 8.00 N 2121 7.00 C 6334 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: 0.76 Conformation dependent library (CDL) restraints added in 227.3 milliseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 73.0% alpha, 2.4% beta 127 base pairs and 223 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.820A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.671A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.802A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.505A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.591A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.500A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.787A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.638A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.727A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.513A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.350A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.413A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.676A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.283A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 409 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 614 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 223 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2176 1.33 - 1.45: 3809 1.45 - 1.57: 5564 1.57 - 1.69: 522 1.69 - 1.81: 24 Bond restraints: 12095 Sorted by residual: bond pdb=" C3' DT J 51 " pdb=" C2' DT J 51 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.49e+01 bond pdb=" C3' DA J 34 " pdb=" C2' DA J 34 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.43e+01 bond pdb=" C3' DT I 60 " pdb=" C2' DT I 60 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.39e+01 bond pdb=" C3' DT J 8 " pdb=" O3' DT J 8 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" C3' DA I 58 " pdb=" O3' DA I 58 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.26e+01 ... (remaining 12090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 16070 1.61 - 3.21: 1286 3.21 - 4.82: 78 4.82 - 6.43: 16 6.43 - 8.04: 1 Bond angle restraints: 17451 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.71 107.75 5.96 9.50e-01 1.11e+00 3.94e+01 angle pdb=" O4' DG I 57 " pdb=" C4' DG I 57 " pdb=" C3' DG I 57 " ideal model delta sigma weight residual 106.00 102.74 3.26 6.00e-01 2.78e+00 2.95e+01 angle pdb=" O4' DG I 47 " pdb=" C4' DG I 47 " pdb=" C3' DG I 47 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.50e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.89 -2.99 6.00e-01 2.78e+00 2.48e+01 angle pdb=" N3 DT I 70 " pdb=" C4 DT I 70 " pdb=" O4 DT I 70 " ideal model delta sigma weight residual 119.90 122.70 -2.80 6.00e-01 2.78e+00 2.18e+01 ... (remaining 17446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 5243 35.14 - 70.28: 1400 70.28 - 105.43: 23 105.43 - 140.57: 3 140.57 - 175.71: 9 Dihedral angle restraints: 6678 sinusoidal: 4495 harmonic: 2183 Sorted by residual: dihedral pdb=" CA TYR G 39 " pdb=" C TYR G 39 " pdb=" N SER G 40 " pdb=" CA SER G 40 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C4' DG J 30 " pdb=" C3' DG J 30 " pdb=" O3' DG J 30 " pdb=" P DA J 31 " ideal model delta sinusoidal sigma weight residual -140.00 35.71 -175.71 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DG I -16 " ideal model delta sinusoidal sigma weight residual -140.00 33.83 -173.83 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1179 0.036 - 0.073: 589 0.073 - 0.109: 161 0.109 - 0.145: 46 0.145 - 0.182: 8 Chirality restraints: 1983 Sorted by residual: chirality pdb=" C3' DA I 58 " pdb=" C4' DA I 58 " pdb=" O3' DA I 58 " pdb=" C2' DA I 58 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" C3' DA I 14 " pdb=" C4' DA I 14 " pdb=" O3' DA I 14 " pdb=" C2' DA I 14 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" C3' DC J 57 " pdb=" C4' DC J 57 " pdb=" O3' DC J 57 " pdb=" C2' DC J 57 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1980 not shown) Planarity restraints: 1305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -24 " -0.027 2.00e-02 2.50e+03 1.18e-02 3.80e+00 pdb=" N9 DA I -24 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I -24 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -24 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA I -24 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -24 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I -24 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -24 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -24 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I -24 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -24 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 16 " 0.027 2.00e-02 2.50e+03 1.10e-02 3.66e+00 pdb=" N9 DG I 16 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DG I 16 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 16 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DG I 16 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG I 16 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG I 16 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DG I 16 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 16 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 16 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 16 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 16 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " 0.025 2.00e-02 2.50e+03 1.08e-02 3.50e+00 pdb=" N9 DG I 28 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " -0.002 2.00e-02 2.50e+03 ... (remaining 1302 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 559 2.70 - 3.25: 9965 3.25 - 3.80: 22342 3.80 - 4.35: 27582 4.35 - 4.90: 39438 Nonbonded interactions: 99886 Sorted by model distance: nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.147 3.040 nonbonded pdb=" OD1 ASP C 90 " pdb=" N GLU C 91 " model vdw 2.185 3.120 nonbonded pdb=" NE ARG A 131 " pdb=" OE2 GLU A 133 " model vdw 2.233 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.251 3.120 ... (remaining 99881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 39 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 13 through 117) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.220 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 16.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.007 0.067 12095 Z= 0.585 Angle : 0.859 8.036 17451 Z= 0.755 Chirality : 0.046 0.182 1983 Planarity : 0.004 0.040 1305 Dihedral : 29.742 175.712 5272 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.67 (0.30), residues: 739 helix: 1.29 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.90 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 32 TYR 0.012 0.002 TYR F 51 PHE 0.024 0.003 PHE C 25 HIS 0.007 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.58 (12095) covalent geometry : angle 0.85857 / 0.75 (17451) hydrogen bonds : bond 0.11327 / 7.77 ( 716) hydrogen bonds : angle 4.81605 / 3.53 ( 1826) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.255 Fit side-chains REVERT: E 59 GLU cc_start: 0.7178 (pp20) cc_final: 0.6897 (pm20) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1486 time to fit residues: 25.5421 Evaluate side-chains 121 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 92 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.141697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103111 restraints weight = 18427.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105573 restraints weight = 11687.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107119 restraints weight = 9117.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.107958 restraints weight = 8018.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107967 restraints weight = 7522.361| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12095 Z= 0.161 Angle : 0.709 8.201 17451 Z= 0.404 Chirality : 0.049 0.344 1983 Planarity : 0.004 0.044 1305 Dihedral : 32.974 175.677 3777 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.12 % Allowed : 8.13 % Favored : 90.75 % 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: 1.30 (0.31), residues: 739 helix: 1.71 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.72 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.018 0.002 TYR C 57 PHE 0.011 0.002 PHE C 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (12095) covalent geometry : angle 0.70935 / 0.40 (17451) hydrogen bonds : bond 0.05640 / 3.74 ( 716) hydrogen bonds : angle 3.43759 / 2.55 ( 1826) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.194 Fit side-chains REVERT: E 59 GLU cc_start: 0.7269 (pp20) cc_final: 0.6996 (pm20) outliers start: 7 outliers final: 6 residues processed: 138 average time/residue: 0.1322 time to fit residues: 23.7455 Evaluate side-chains 134 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.140805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101905 restraints weight = 18576.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104326 restraints weight = 11823.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105853 restraints weight = 9229.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.106678 restraints weight = 8122.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106794 restraints weight = 7618.567| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12095 Z= 0.193 Angle : 0.708 9.360 17451 Z= 0.402 Chirality : 0.049 0.352 1983 Planarity : 0.004 0.040 1305 Dihedral : 33.023 175.144 3777 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.44 % Allowed : 11.16 % Favored : 87.40 % 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: 1.52 (0.31), residues: 739 helix: 1.93 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.73 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 35 TYR 0.011 0.002 TYR F 51 PHE 0.014 0.003 PHE A 67 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (12095) covalent geometry : angle 0.70829 / 0.40 (17451) hydrogen bonds : bond 0.05638 / 3.73 ( 716) hydrogen bonds : angle 3.37591 / 2.51 ( 1826) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.332 Fit side-chains REVERT: E 59 GLU cc_start: 0.7282 (pp20) cc_final: 0.7055 (pm20) outliers start: 9 outliers final: 8 residues processed: 130 average time/residue: 0.1439 time to fit residues: 24.5595 Evaluate side-chains 132 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 94 optimal weight: 20.0000 chunk 31 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 28 optimal weight: 0.0170 chunk 58 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.141228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102103 restraints weight = 18722.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.104736 restraints weight = 11525.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106385 restraints weight = 8846.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107243 restraints weight = 7705.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107392 restraints weight = 7221.958| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12095 Z= 0.170 Angle : 0.678 7.785 17451 Z= 0.389 Chirality : 0.048 0.347 1983 Planarity : 0.004 0.039 1305 Dihedral : 33.018 176.005 3777 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.39 % Allowed : 11.64 % Favored : 85.96 % 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: 1.69 (0.31), residues: 739 helix: 2.09 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.81 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.016 0.002 TYR C 57 PHE 0.013 0.002 PHE A 67 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (12095) covalent geometry : angle 0.67835 / 0.39 (17451) hydrogen bonds : bond 0.05318 / 3.52 ( 716) hydrogen bonds : angle 3.29028 / 2.45 ( 1826) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.327 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 135 average time/residue: 0.1399 time to fit residues: 24.8266 Evaluate side-chains 140 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 86 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.139753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.100663 restraints weight = 18630.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103025 restraints weight = 11971.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.104488 restraints weight = 9459.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105209 restraints weight = 8386.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105209 restraints weight = 7903.855| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12095 Z= 0.236 Angle : 0.724 8.007 17451 Z= 0.407 Chirality : 0.050 0.362 1983 Planarity : 0.005 0.041 1305 Dihedral : 33.081 175.912 3777 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.07 % Allowed : 12.60 % Favored : 85.33 % 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: 1.49 (0.30), residues: 739 helix: 1.92 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.80 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.015 0.002 TYR C 39 PHE 0.015 0.003 PHE G 25 HIS 0.007 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.24 (12095) covalent geometry : angle 0.72398 / 0.41 (17451) hydrogen bonds : bond 0.05822 / 3.86 ( 716) hydrogen bonds : angle 3.33995 / 2.47 ( 1826) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.303 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 127 average time/residue: 0.1416 time to fit residues: 24.0817 Evaluate side-chains 130 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.141837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.103182 restraints weight = 18658.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.105698 restraints weight = 11715.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107241 restraints weight = 9077.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107967 restraints weight = 7989.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.108030 restraints weight = 7513.999| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12095 Z= 0.149 Angle : 0.662 7.561 17451 Z= 0.381 Chirality : 0.047 0.343 1983 Planarity : 0.004 0.040 1305 Dihedral : 33.010 177.372 3777 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 14.19 % Favored : 83.73 % 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: 1.85 (0.30), residues: 739 helix: 2.16 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.68 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 81 TYR 0.014 0.002 TYR C 57 PHE 0.014 0.002 PHE A 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (12095) covalent geometry : angle 0.66176 / 0.38 (17451) hydrogen bonds : bond 0.04836 / 3.21 ( 716) hydrogen bonds : angle 3.14514 / 2.34 ( 1826) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.323 Fit side-chains REVERT: H 90 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7348 (mp0) outliers start: 13 outliers final: 10 residues processed: 136 average time/residue: 0.1432 time to fit residues: 25.8485 Evaluate side-chains 134 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 51 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 44 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.141709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102818 restraints weight = 18628.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.105435 restraints weight = 11455.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107045 restraints weight = 8798.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.107789 restraints weight = 7718.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.107789 restraints weight = 7255.883| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12095 Z= 0.157 Angle : 0.661 7.751 17451 Z= 0.378 Chirality : 0.047 0.353 1983 Planarity : 0.004 0.040 1305 Dihedral : 32.957 178.113 3777 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.23 % Allowed : 14.67 % Favored : 83.09 % 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 (0.31), residues: 739 helix: 2.32 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.67 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 83 TYR 0.013 0.001 TYR C 57 PHE 0.015 0.002 PHE A 67 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (12095) covalent geometry : angle 0.66085 / 0.38 (17451) hydrogen bonds : bond 0.04898 / 3.26 ( 716) hydrogen bonds : angle 3.12733 / 2.32 ( 1826) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.279 Fit side-chains REVERT: H 90 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7300 (mt-10) outliers start: 14 outliers final: 10 residues processed: 129 average time/residue: 0.1227 time to fit residues: 21.1018 Evaluate side-chains 131 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 57 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.142570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.103594 restraints weight = 18583.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106202 restraints weight = 11453.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.107825 restraints weight = 8810.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108661 restraints weight = 7725.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109135 restraints weight = 7239.092| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12095 Z= 0.140 Angle : 0.648 7.997 17451 Z= 0.372 Chirality : 0.046 0.344 1983 Planarity : 0.004 0.040 1305 Dihedral : 32.935 178.497 3777 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.91 % Allowed : 15.31 % Favored : 82.78 % 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 (0.31), residues: 739 helix: 2.38 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.55 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.012 0.001 TYR C 57 PHE 0.014 0.002 PHE A 67 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (12095) covalent geometry : angle 0.64776 / 0.37 (17451) hydrogen bonds : bond 0.04639 / 3.09 ( 716) hydrogen bonds : angle 3.06890 / 2.28 ( 1826) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.325 Fit side-chains REVERT: H 90 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7294 (mt-10) outliers start: 12 outliers final: 8 residues processed: 132 average time/residue: 0.1287 time to fit residues: 22.7265 Evaluate side-chains 130 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 39 optimal weight: 0.0170 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 52 optimal weight: 10.0000 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.142361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.103287 restraints weight = 18446.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.105879 restraints weight = 11378.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.107437 restraints weight = 8801.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.108328 restraints weight = 7727.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108544 restraints weight = 7243.419| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12095 Z= 0.148 Angle : 0.646 7.646 17451 Z= 0.371 Chirality : 0.046 0.351 1983 Planarity : 0.004 0.040 1305 Dihedral : 32.903 179.037 3777 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.75 % Allowed : 16.11 % Favored : 82.14 % 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: 2.20 (0.31), residues: 739 helix: 2.41 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 83 TYR 0.010 0.001 TYR C 57 PHE 0.014 0.002 PHE A 67 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (12095) covalent geometry : angle 0.64561 / 0.37 (17451) hydrogen bonds : bond 0.04655 / 3.11 ( 716) hydrogen bonds : angle 3.03797 / 2.25 ( 1826) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.224 Fit side-chains REVERT: H 90 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7357 (mt-10) outliers start: 11 outliers final: 10 residues processed: 128 average time/residue: 0.1315 time to fit residues: 22.4142 Evaluate side-chains 132 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.141642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.102500 restraints weight = 18744.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105119 restraints weight = 11606.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106694 restraints weight = 8921.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107422 restraints weight = 7828.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107422 restraints weight = 7342.239| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12095 Z= 0.170 Angle : 0.664 8.938 17451 Z= 0.377 Chirality : 0.047 0.353 1983 Planarity : 0.004 0.039 1305 Dihedral : 32.927 179.193 3777 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.91 % Allowed : 15.95 % Favored : 82.14 % 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: 2.10 (0.30), residues: 739 helix: 2.35 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.54 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 83 TYR 0.019 0.002 TYR C 57 PHE 0.012 0.002 PHE A 67 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (12095) covalent geometry : angle 0.66416 / 0.38 (17451) hydrogen bonds : bond 0.04925 / 3.29 ( 716) hydrogen bonds : angle 3.10290 / 2.30 ( 1826) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.310 Fit side-chains REVERT: H 90 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7347 (mt-10) outliers start: 12 outliers final: 10 residues processed: 130 average time/residue: 0.1419 time to fit residues: 24.5943 Evaluate side-chains 134 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.142145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103105 restraints weight = 18669.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105713 restraints weight = 11514.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.107332 restraints weight = 8873.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108070 restraints weight = 7756.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108134 restraints weight = 7273.164| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12095 Z= 0.149 Angle : 0.653 8.620 17451 Z= 0.373 Chirality : 0.046 0.344 1983 Planarity : 0.004 0.041 1305 Dihedral : 32.918 179.384 3777 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.75 % Allowed : 16.27 % Favored : 81.98 % 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: 2.20 (0.31), residues: 739 helix: 2.43 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -1.48 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 83 TYR 0.017 0.001 TYR C 57 PHE 0.013 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (12095) covalent geometry : angle 0.65321 / 0.37 (17451) hydrogen bonds : bond 0.04759 / 3.18 ( 716) hydrogen bonds : angle 3.07297 / 2.28 ( 1826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1648.09 seconds wall clock time: 29 minutes 16.22 seconds (1756.22 seconds total)