Starting phenix.real_space_refine on Fri Jul 3 05:39:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v27_42900/07_2026/8v27_42900_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v27_42900/07_2026/8v27_42900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v27_42900/07_2026/8v27_42900_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v27_42900/07_2026/8v27_42900_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v27_42900/07_2026/8v27_42900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v27_42900/07_2026/8v27_42900.map" } resolution = 3.34 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= 0.002 sd= 0.019 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 288 5.49 5 S 16 5.16 5 C 7063 2.51 5 N 2387 2.21 5 O 2935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12689 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 764 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 604 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU K 73 " occ=0.79 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.79 residue: pdb=" N ARG K 74 " occ=0.72 ... (9 atoms not shown) pdb=" NH2 ARG K 74 " occ=0.72 Time building chain proxies: 2.67, per 1000 atoms: 0.21 Number of scatterers: 12689 At special positions: 0 Unit cell: (98.94, 122.22, 118.34, 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 16 16.00 P 288 15.00 O 2935 8.00 N 2387 7.00 C 7063 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: 0.97 Conformation dependent library (CDL) restraints added in 361.9 milliseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1592 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 66.4% alpha, 4.5% beta 138 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.870A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.809A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.626A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.211A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.527A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.522A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.673A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.515A 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 77 removed outlier: 3.596A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.770A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.203A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.529A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.546A 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 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.582A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.660A pdb=" N ALA H 121 " --> pdb=" O CYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 34 removed outlier: 3.819A pdb=" N VAL K 26 " --> pdb=" O THR K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 removed outlier: 3.901A pdb=" N TYR K 59 " --> pdb=" O THR K 55 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 55 through 60' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.049A 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: 7.447A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.807A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.352A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 13 through 16 removed outlier: 4.127A pdb=" N SER K 65 " --> pdb=" O GLN K 2 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2807 1.34 - 1.46: 4102 1.46 - 1.57: 5986 1.57 - 1.69: 576 1.69 - 1.81: 27 Bond restraints: 13498 Sorted by residual: bond pdb=" C1' DT J -72 " pdb=" N1 DT J -72 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.36e+01 bond pdb=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.468 1.387 0.081 1.40e-02 5.10e+03 3.35e+01 bond pdb=" C1' DT I -72 " pdb=" N1 DT I -72 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.29e+01 bond pdb=" C1' DG J -70 " pdb=" N9 DG J -70 " ideal model delta sigma weight residual 1.468 1.388 0.080 1.40e-02 5.10e+03 3.26e+01 bond pdb=" C1' DC I 70 " pdb=" N1 DC I 70 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.87e+01 ... (remaining 13493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 19280 2.59 - 5.17: 170 5.17 - 7.76: 13 7.76 - 10.35: 2 10.35 - 12.93: 1 Bond angle restraints: 19466 Sorted by residual: angle pdb=" C3' DG J 71 " pdb=" O3' DG J 71 " pdb=" P DA J 72 " ideal model delta sigma weight residual 120.20 107.27 12.93 1.50e+00 4.44e-01 7.43e+01 angle pdb=" C3' DC J 70 " pdb=" O3' DC J 70 " pdb=" P DG J 71 " ideal model delta sigma weight residual 120.20 112.08 8.12 1.50e+00 4.44e-01 2.93e+01 angle pdb=" C3' DG I 71 " pdb=" O3' DG I 71 " pdb=" P DA I 72 " ideal model delta sigma weight residual 120.20 112.93 7.27 1.50e+00 4.44e-01 2.35e+01 angle pdb=" O4' DG J -49 " pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.20e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 19461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 6025 35.68 - 71.36: 1373 71.36 - 107.04: 5 107.04 - 142.72: 4 142.72 - 178.39: 1 Dihedral angle restraints: 7408 sinusoidal: 4945 harmonic: 2463 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.39 -178.39 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PRO K 37 " pdb=" C PRO K 37 " pdb=" N PRO K 38 " pdb=" CA PRO K 38 " ideal model delta harmonic sigma weight residual -180.00 -161.94 -18.06 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 92.49 127.51 1 3.50e+01 8.16e-04 1.26e+01 ... (remaining 7405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2110 0.093 - 0.187: 104 0.187 - 0.280: 0 0.280 - 0.374: 1 0.374 - 0.467: 4 Chirality restraints: 2219 Sorted by residual: chirality pdb=" P DG I 71 " pdb=" OP1 DG I 71 " pdb=" OP2 DG I 71 " pdb=" O5' DG I 71 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" P DG J 71 " pdb=" OP1 DG J 71 " pdb=" OP2 DG J 71 " pdb=" O5' DG J 71 " both_signs ideal model delta sigma weight residual True 2.34 -2.78 -0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" P DA J 72 " pdb=" OP1 DA J 72 " pdb=" OP2 DA J 72 " pdb=" O5' DA J 72 " both_signs ideal model delta sigma weight residual True 2.34 -2.78 -0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 2216 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C ASP F 24 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 65 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" CG ASP H 65 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP H 65 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP H 65 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 24 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" CG ASP F 24 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP F 24 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP F 24 " 0.012 2.00e-02 2.50e+03 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 859 2.74 - 3.28: 10859 3.28 - 3.82: 22686 3.82 - 4.36: 26706 4.36 - 4.90: 39729 Nonbonded interactions: 100839 Sorted by model distance: nonbonded pdb=" NE2 GLN K 31 " pdb=" O ILE K 36 " model vdw 2.196 3.120 nonbonded pdb=" N MET K 1 " pdb=" OE2 GLU K 16 " model vdw 2.200 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.246 3.120 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.251 3.040 nonbonded pdb=" O GLN K 62 " pdb=" OG SER K 65 " model vdw 2.260 3.040 ... (remaining 100834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 26 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.850 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 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 0.081 13498 Z= 0.524 Angle : 0.742 12.932 19466 Z= 0.645 Chirality : 0.048 0.467 2219 Planarity : 0.004 0.040 1463 Dihedral : 27.255 178.394 5816 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.42 % Allowed : 21.32 % Favored : 78.26 % 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: 2.63 (0.30), residues: 831 helix: 3.22 (0.22), residues: 530 sheet: 0.47 (1.08), residues: 26 loop : -1.27 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 30 TYR 0.011 0.001 TYR K 59 PHE 0.024 0.001 PHE K 4 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.52 (13498) covalent geometry : angle 0.74216 / 0.64 (19466) hydrogen bonds : bond 0.11782 / 8.01 ( 773) hydrogen bonds : angle 3.66615 / 2.56 ( 1944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 141 average time/residue: 0.1395 time to fit residues: 26.1426 Evaluate side-chains 142 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.063804 restraints weight = 29007.053| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.09 r_work: 0.2692 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13498 Z= 0.151 Angle : 0.577 6.880 19466 Z= 0.361 Chirality : 0.043 0.236 2219 Planarity : 0.004 0.033 1463 Dihedral : 29.550 175.354 4121 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.38 % Allowed : 19.64 % Favored : 77.98 % 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: 2.80 (0.30), residues: 831 helix: 3.26 (0.22), residues: 540 sheet: 0.39 (1.04), residues: 26 loop : -1.16 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 30 TYR 0.008 0.001 TYR K 59 PHE 0.007 0.001 PHE F 61 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.15 (13498) covalent geometry : angle 0.57737 / 0.36 (19466) hydrogen bonds : bond 0.05763 / 3.78 ( 773) hydrogen bonds : angle 3.15199 / 2.24 ( 1944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8661 (mttp) REVERT: F 24 ASP cc_start: 0.8556 (p0) cc_final: 0.8240 (p0) outliers start: 17 outliers final: 9 residues processed: 153 average time/residue: 0.1230 time to fit residues: 25.2716 Evaluate side-chains 145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 13 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN K 2 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.091460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061653 restraints weight = 28954.876| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.09 r_work: 0.2649 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13498 Z= 0.174 Angle : 0.582 7.070 19466 Z= 0.356 Chirality : 0.043 0.233 2219 Planarity : 0.004 0.034 1463 Dihedral : 29.702 175.506 4117 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.51 % Allowed : 20.76 % Favored : 75.74 % 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: 2.77 (0.30), residues: 831 helix: 3.29 (0.22), residues: 539 sheet: 0.55 (1.04), residues: 26 loop : -1.29 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 54 TYR 0.009 0.001 TYR K 59 PHE 0.010 0.002 PHE K 4 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (13498) covalent geometry : angle 0.58219 / 0.36 (19466) hydrogen bonds : bond 0.06257 / 4.11 ( 773) hydrogen bonds : angle 3.15676 / 2.26 ( 1944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8676 (mttp) REVERT: C 62 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8285 (mt) REVERT: F 24 ASP cc_start: 0.8611 (p0) cc_final: 0.8235 (p0) REVERT: K 24 GLU cc_start: 0.9478 (OUTLIER) cc_final: 0.9194 (mp0) REVERT: K 42 ARG cc_start: 0.8151 (tpm170) cc_final: 0.7477 (tpm170) REVERT: K 51 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7029 (pm20) outliers start: 25 outliers final: 15 residues processed: 151 average time/residue: 0.1316 time to fit residues: 26.3640 Evaluate side-chains 149 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 4 PHE Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.062638 restraints weight = 28707.237| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.08 r_work: 0.2672 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13498 Z= 0.147 Angle : 0.569 8.381 19466 Z= 0.348 Chirality : 0.042 0.233 2219 Planarity : 0.004 0.040 1463 Dihedral : 29.736 175.381 4114 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.95 % Allowed : 21.04 % Favored : 76.02 % 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: 2.82 (0.30), residues: 831 helix: 3.33 (0.22), residues: 539 sheet: 0.48 (1.02), residues: 26 loop : -1.28 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.006 0.001 TYR H 37 PHE 0.009 0.001 PHE K 4 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.15 (13498) covalent geometry : angle 0.56885 / 0.35 (19466) hydrogen bonds : bond 0.05747 / 3.78 ( 773) hydrogen bonds : angle 3.04376 / 2.17 ( 1944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8691 (mttp) REVERT: F 24 ASP cc_start: 0.8578 (p0) cc_final: 0.8188 (p0) REVERT: K 24 GLU cc_start: 0.9474 (OUTLIER) cc_final: 0.9174 (mp0) REVERT: K 40 GLN cc_start: 0.9109 (mp10) cc_final: 0.8754 (mm-40) REVERT: K 42 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7642 (tpm170) REVERT: K 51 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6764 (pm20) outliers start: 21 outliers final: 15 residues processed: 151 average time/residue: 0.1203 time to fit residues: 24.4420 Evaluate side-chains 153 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 4 PHE Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 42 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 0.0070 chunk 49 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.063896 restraints weight = 29036.456| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.10 r_work: 0.2699 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13498 Z= 0.140 Angle : 0.549 6.735 19466 Z= 0.338 Chirality : 0.041 0.230 2219 Planarity : 0.004 0.041 1463 Dihedral : 29.817 174.996 4114 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.81 % Allowed : 21.46 % Favored : 75.74 % 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: 2.86 (0.30), residues: 831 helix: 3.39 (0.22), residues: 539 sheet: 0.16 (1.02), residues: 26 loop : -1.30 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 42 TYR 0.006 0.001 TYR H 37 PHE 0.011 0.001 PHE K 4 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.14 (13498) covalent geometry : angle 0.54910 / 0.34 (19466) hydrogen bonds : bond 0.05250 / 3.46 ( 773) hydrogen bonds : angle 2.94736 / 2.10 ( 1944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8681 (mttp) REVERT: F 24 ASP cc_start: 0.8615 (p0) cc_final: 0.8213 (p0) REVERT: G 81 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.9097 (tpt170) REVERT: K 2 GLN cc_start: 0.8509 (tp40) cc_final: 0.8202 (tp40) REVERT: K 42 ARG cc_start: 0.8330 (tpm170) cc_final: 0.7961 (tpm170) outliers start: 20 outliers final: 13 residues processed: 158 average time/residue: 0.1255 time to fit residues: 26.6540 Evaluate side-chains 152 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 81 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 43 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 8.9990 chunk 26 optimal weight: 0.0670 chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 0.0000 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 2 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.064846 restraints weight = 28988.583| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.12 r_work: 0.2728 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13498 Z= 0.135 Angle : 0.545 8.002 19466 Z= 0.334 Chirality : 0.040 0.229 2219 Planarity : 0.004 0.046 1463 Dihedral : 29.875 174.790 4114 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.66 % Allowed : 23.00 % Favored : 74.33 % 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: 2.92 (0.30), residues: 831 helix: 3.46 (0.22), residues: 539 sheet: 0.31 (1.02), residues: 26 loop : -1.36 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 54 TYR 0.005 0.001 TYR H 37 PHE 0.012 0.001 PHE A 78 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.14 (13498) covalent geometry : angle 0.54492 / 0.33 (19466) hydrogen bonds : bond 0.04811 / 3.18 ( 773) hydrogen bonds : angle 2.86843 / 2.04 ( 1944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8680 (mttp) REVERT: F 24 ASP cc_start: 0.8584 (p0) cc_final: 0.8251 (p0) REVERT: K 40 GLN cc_start: 0.9009 (mp10) cc_final: 0.8550 (mm-40) REVERT: K 42 ARG cc_start: 0.8310 (tpm170) cc_final: 0.7803 (tpm170) REVERT: K 51 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6558 (pm20) outliers start: 19 outliers final: 13 residues processed: 161 average time/residue: 0.1191 time to fit residues: 25.8343 Evaluate side-chains 151 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 13 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.092923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.063451 restraints weight = 28891.457| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.11 r_work: 0.2686 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13498 Z= 0.153 Angle : 0.559 6.980 19466 Z= 0.337 Chirality : 0.041 0.230 2219 Planarity : 0.004 0.039 1463 Dihedral : 29.949 174.575 4114 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.23 % Allowed : 23.14 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.30), residues: 831 helix: 3.41 (0.22), residues: 540 sheet: 0.11 (1.03), residues: 26 loop : -1.46 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 30 TYR 0.016 0.001 TYR K 59 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (13498) covalent geometry : angle 0.55901 / 0.34 (19466) hydrogen bonds : bond 0.05483 / 3.61 ( 773) hydrogen bonds : angle 2.96699 / 2.11 ( 1944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8684 (mttp) REVERT: E 59 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: F 24 ASP cc_start: 0.8565 (p0) cc_final: 0.8130 (p0) REVERT: F 84 MET cc_start: 0.8651 (mmm) cc_final: 0.8256 (mmm) REVERT: K 24 GLU cc_start: 0.9482 (OUTLIER) cc_final: 0.9222 (mp0) REVERT: K 40 GLN cc_start: 0.9011 (mp10) cc_final: 0.8653 (mm-40) REVERT: K 42 ARG cc_start: 0.8357 (tpm170) cc_final: 0.7753 (tpm170) REVERT: K 49 GLN cc_start: 0.8569 (mm-40) cc_final: 0.7996 (mm-40) REVERT: K 51 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6402 (pm20) outliers start: 23 outliers final: 18 residues processed: 155 average time/residue: 0.1145 time to fit residues: 24.2054 Evaluate side-chains 158 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 76 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 102 optimal weight: 50.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.091602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.061974 restraints weight = 28564.264| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.09 r_work: 0.2654 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13498 Z= 0.168 Angle : 0.586 10.100 19466 Z= 0.347 Chirality : 0.042 0.236 2219 Planarity : 0.004 0.039 1463 Dihedral : 30.009 174.335 4114 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.51 % Allowed : 23.84 % Favored : 72.65 % 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: 2.72 (0.30), residues: 831 helix: 3.36 (0.22), residues: 540 sheet: 0.10 (1.03), residues: 26 loop : -1.56 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 30 TYR 0.013 0.001 TYR K 59 PHE 0.015 0.002 PHE K 4 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (13498) covalent geometry : angle 0.58627 / 0.35 (19466) hydrogen bonds : bond 0.06073 / 4.00 ( 773) hydrogen bonds : angle 3.05438 / 2.17 ( 1944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8677 (mttp) REVERT: C 62 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8325 (mt) REVERT: F 24 ASP cc_start: 0.8603 (p0) cc_final: 0.8121 (p0) REVERT: K 15 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7351 (mm) REVERT: K 24 GLU cc_start: 0.9480 (OUTLIER) cc_final: 0.9217 (mp0) REVERT: K 42 ARG cc_start: 0.8303 (tpm170) cc_final: 0.7606 (tpm170) REVERT: K 49 GLN cc_start: 0.8531 (mm-40) cc_final: 0.7942 (mm-40) REVERT: K 51 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6248 (pm20) outliers start: 25 outliers final: 17 residues processed: 148 average time/residue: 0.1162 time to fit residues: 23.7336 Evaluate side-chains 152 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 4 PHE Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 76 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 9 optimal weight: 0.0670 chunk 103 optimal weight: 0.0770 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.092531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.063052 restraints weight = 28735.973| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.09 r_work: 0.2679 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13498 Z= 0.139 Angle : 0.567 9.506 19466 Z= 0.341 Chirality : 0.042 0.235 2219 Planarity : 0.004 0.040 1463 Dihedral : 30.002 174.511 4114 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.81 % Allowed : 24.68 % Favored : 72.51 % 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: 2.75 (0.30), residues: 831 helix: 3.37 (0.22), residues: 540 sheet: 0.02 (1.02), residues: 26 loop : -1.52 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 30 TYR 0.015 0.001 TYR K 59 PHE 0.012 0.001 PHE K 4 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.14 (13498) covalent geometry : angle 0.56656 / 0.34 (19466) hydrogen bonds : bond 0.05601 / 3.68 ( 773) hydrogen bonds : angle 2.96611 / 2.10 ( 1944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8693 (mttp) REVERT: F 24 ASP cc_start: 0.8591 (p0) cc_final: 0.8117 (p0) REVERT: F 84 MET cc_start: 0.8628 (mmm) cc_final: 0.8333 (mmm) REVERT: K 2 GLN cc_start: 0.8532 (tp40) cc_final: 0.8246 (tp40) REVERT: K 42 ARG cc_start: 0.8298 (tpm170) cc_final: 0.7665 (tpm170) REVERT: K 49 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8014 (mm-40) REVERT: K 51 GLU cc_start: 0.6870 (tm-30) cc_final: 0.6296 (pm20) outliers start: 20 outliers final: 15 residues processed: 152 average time/residue: 0.1181 time to fit residues: 24.5575 Evaluate side-chains 153 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 4 PHE Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 76 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.090291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.060249 restraints weight = 28778.172| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.08 r_work: 0.2615 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13498 Z= 0.186 Angle : 0.612 10.005 19466 Z= 0.358 Chirality : 0.044 0.236 2219 Planarity : 0.004 0.040 1463 Dihedral : 30.074 174.466 4114 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.09 % Allowed : 24.54 % Favored : 72.37 % 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: 2.57 (0.30), residues: 831 helix: 3.22 (0.22), residues: 543 sheet: -0.02 (1.01), residues: 26 loop : -1.64 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 30 TYR 0.013 0.001 TYR K 59 PHE 0.009 0.002 PHE F 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 (13498) covalent geometry : angle 0.61231 / 0.36 (19466) hydrogen bonds : bond 0.06784 / 4.46 ( 773) hydrogen bonds : angle 3.17039 / 2.27 ( 1944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8694 (mttp) REVERT: C 62 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8513 (mt) REVERT: E 59 GLU cc_start: 0.8046 (pm20) cc_final: 0.7664 (pm20) REVERT: F 24 ASP cc_start: 0.8601 (p0) cc_final: 0.8131 (p0) REVERT: K 2 GLN cc_start: 0.8588 (tp40) cc_final: 0.8245 (tp40) REVERT: K 24 GLU cc_start: 0.9450 (OUTLIER) cc_final: 0.9176 (mp0) REVERT: K 42 ARG cc_start: 0.8332 (tpm170) cc_final: 0.7706 (tpm170) REVERT: K 49 GLN cc_start: 0.8496 (mm-40) cc_final: 0.7962 (mm-40) REVERT: K 51 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6437 (pm20) outliers start: 22 outliers final: 18 residues processed: 146 average time/residue: 0.1340 time to fit residues: 26.6621 Evaluate side-chains 153 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 76 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 102 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.086859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.056374 restraints weight = 28639.474| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.09 r_work: 0.2523 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13498 Z= 0.289 Angle : 0.723 10.076 19466 Z= 0.407 Chirality : 0.050 0.252 2219 Planarity : 0.005 0.041 1463 Dihedral : 30.207 174.623 4114 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.23 % Allowed : 24.82 % Favored : 71.95 % 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: 1.95 (0.29), residues: 831 helix: 2.75 (0.22), residues: 542 sheet: -0.22 (0.98), residues: 26 loop : -1.88 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 30 TYR 0.017 0.002 TYR E 54 PHE 0.017 0.002 PHE D 67 HIS 0.005 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.29 (13498) covalent geometry : angle 0.72282 / 0.41 (19466) hydrogen bonds : bond 0.08922 / 5.89 ( 773) hydrogen bonds : angle 3.56067 / 2.57 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2204.55 seconds wall clock time: 38 minutes 27.54 seconds (2307.54 seconds total)