Starting phenix.real_space_refine on Sat Oct 11 06:26:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v27_42900/10_2025/8v27_42900_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v27_42900/10_2025/8v27_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_42900/10_2025/8v27_42900_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v27_42900/10_2025/8v27_42900_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v27_42900/10_2025/8v27_42900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v27_42900/10_2025/8v27_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-2.0-5842/lib/python3.9/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: 2.64, 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: 1.01 Conformation dependent library (CDL) restraints added in 350.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.10 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: 2.43 Time building geometry restraints manager: 1.39 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' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.460 1.387 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1' DG J -70 " pdb=" N9 DG J -70 " ideal model delta sigma weight residual 1.460 1.388 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" N LEU K 73 " pdb=" CA LEU K 73 " ideal model delta sigma weight residual 1.459 1.485 -0.027 1.16e-02 7.43e+03 5.28e+00 bond pdb=" N ARG K 74 " pdb=" CA ARG K 74 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.98e+00 bond pdb=" N CYS D 117 " pdb=" CA CYS D 117 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.69e+00 ... (remaining 13493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 19349 2.59 - 5.17: 101 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=" CA GLN A 76 " pdb=" CB GLN A 76 " pdb=" CG GLN A 76 " ideal model delta sigma weight residual 114.10 122.51 -8.41 2.00e+00 2.50e-01 1.77e+01 angle pdb=" CA LYS H 113 " pdb=" CB LYS H 113 " pdb=" CG LYS H 113 " ideal model delta sigma weight residual 114.10 121.54 -7.44 2.00e+00 2.50e-01 1.39e+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 - 0.091: 2156 0.091 - 0.183: 58 0.183 - 0.274: 0 0.274 - 0.365: 1 0.365 - 0.457: 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 2.35 -2.80 -0.46 2.00e-01 2.50e+01 5.22e+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 2.35 -2.78 -0.44 2.00e-01 2.50e+01 4.80e+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 2.35 -2.78 -0.44 2.00e-01 2.50e+01 4.75e+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: 1.160 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: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.810 Find NCS groups from input model: 0.130 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13498 Z= 0.180 Angle : 0.592 12.932 19466 Z= 0.357 Chirality : 0.039 0.457 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 aren 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 covalent geometry : bond 0.00370 (13498) covalent geometry : angle 0.59198 (19466) hydrogen bonds : bond 0.11782 ( 773) hydrogen bonds : angle 3.66615 ( 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 : 0.595 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: 0.1614 time to fit residues: 30.2600 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 : 0.341 ------------------------------------------------------------------------------- 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: 6.9990 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.063811 restraints weight = 29128.412| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.11 r_work: 0.2696 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 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 = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13498 Z= 0.154 Angle : 0.529 5.884 19466 Z= 0.322 Chirality : 0.033 0.154 2219 Planarity : 0.004 0.035 1463 Dihedral : 29.226 177.294 4121 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.66 % Allowed : 18.79 % Favored : 78.54 % 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 aren not related in a simple way. whole: 2.88 (0.30), residues: 831 helix: 3.35 (0.22), residues: 539 sheet: 0.41 (1.07), residues: 26 loop : -1.17 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 30 TYR 0.011 0.001 TYR K 59 PHE 0.008 0.001 PHE K 4 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00322 (13498) covalent geometry : angle 0.52931 (19466) hydrogen bonds : bond 0.04970 ( 773) hydrogen bonds : angle 2.99479 ( 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 161 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8654 (mttp) REVERT: F 24 ASP cc_start: 0.8576 (p0) cc_final: 0.8238 (p0) REVERT: F 84 MET cc_start: 0.8572 (tpp) cc_final: 0.8226 (mmm) REVERT: K 24 GLU cc_start: 0.9475 (pt0) cc_final: 0.9204 (mp0) outliers start: 19 outliers final: 11 residues processed: 155 average time/residue: 0.1554 time to fit residues: 31.9766 Evaluate side-chains 147 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain D residue 29 THR 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 2 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 = 0.3381 r_free = 0.3381 target = 0.090300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.060336 restraints weight = 28874.382| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.09 r_work: 0.2607 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13498 Z= 0.203 Angle : 0.557 5.953 19466 Z= 0.337 Chirality : 0.035 0.139 2219 Planarity : 0.004 0.035 1463 Dihedral : 29.374 177.643 4114 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.95 % Allowed : 20.34 % Favored : 76.72 % 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 aren not related in a simple way. whole: 2.71 (0.30), residues: 831 helix: 3.22 (0.22), residues: 542 sheet: 0.73 (1.09), residues: 26 loop : -1.36 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.010 0.001 TYR E 54 PHE 0.012 0.002 PHE K 4 HIS 0.004 0.001 HIS K 68 Details of bonding type rmsd covalent geometry : bond 0.00455 (13498) covalent geometry : angle 0.55725 (19466) hydrogen bonds : bond 0.06452 ( 773) hydrogen bonds : angle 3.13577 ( 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 158 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8679 (mttp) REVERT: C 62 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8462 (mt) REVERT: F 24 ASP cc_start: 0.8642 (p0) cc_final: 0.8276 (p0) REVERT: K 24 GLU cc_start: 0.9452 (OUTLIER) cc_final: 0.9212 (mp0) REVERT: K 40 GLN cc_start: 0.9099 (mp10) cc_final: 0.8753 (mm-40) REVERT: K 42 ARG cc_start: 0.8215 (tpm170) cc_final: 0.7591 (tpm170) outliers start: 21 outliers final: 13 residues processed: 151 average time/residue: 0.1505 time to fit residues: 30.0605 Evaluate side-chains 151 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 D residue 119 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 24 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 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 = 0.3390 r_free = 0.3390 target = 0.090758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.060925 restraints weight = 28558.327| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.09 r_work: 0.2626 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13498 Z= 0.167 Angle : 0.544 6.362 19466 Z= 0.329 Chirality : 0.034 0.138 2219 Planarity : 0.004 0.040 1463 Dihedral : 29.373 177.413 4114 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.07 % Allowed : 20.48 % Favored : 75.46 % 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 aren not related in a simple way. whole: 2.75 (0.30), residues: 831 helix: 3.26 (0.22), residues: 542 sheet: 0.65 (1.09), residues: 26 loop : -1.36 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.010 0.001 TYR K 59 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00358 (13498) covalent geometry : angle 0.54378 (19466) hydrogen bonds : bond 0.05962 ( 773) hydrogen bonds : angle 3.05441 ( 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 169 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8698 (mttp) REVERT: C 42 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7855 (ptp-170) REVERT: C 62 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8370 (mt) REVERT: D 28 LYS cc_start: 0.6108 (OUTLIER) cc_final: 0.5861 (mppt) REVERT: F 24 ASP cc_start: 0.8641 (p0) cc_final: 0.8319 (p0) REVERT: K 24 GLU cc_start: 0.9467 (OUTLIER) cc_final: 0.9209 (mp0) REVERT: K 42 ARG cc_start: 0.8390 (tpm170) cc_final: 0.7832 (tpm170) REVERT: K 76 CYS cc_start: 0.5628 (OUTLIER) cc_final: 0.5293 (p) outliers start: 29 outliers final: 18 residues processed: 157 average time/residue: 0.1517 time to fit residues: 31.4427 Evaluate side-chains 161 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 42 ARG 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 28 LYS 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 73 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 24 GLU Chi-restraints excluded: chain K residue 76 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 9 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3405 r_free = 0.3405 target = 0.091609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.062014 restraints weight = 28900.390| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.10 r_work: 0.2652 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13498 Z= 0.158 Angle : 0.535 8.437 19466 Z= 0.324 Chirality : 0.033 0.129 2219 Planarity : 0.004 0.041 1463 Dihedral : 29.365 177.080 4114 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.93 % Allowed : 21.18 % Favored : 74.89 % 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 aren not related in a simple way. whole: 2.81 (0.30), residues: 831 helix: 3.38 (0.22), residues: 539 sheet: 0.22 (0.99), residues: 26 loop : -1.39 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.006 0.001 TYR H 37 PHE 0.009 0.001 PHE K 4 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00334 (13498) covalent geometry : angle 0.53494 (19466) hydrogen bonds : bond 0.05399 ( 773) hydrogen bonds : angle 2.93541 ( 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 167 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8695 (mttp) REVERT: D 28 LYS cc_start: 0.6118 (mppt) cc_final: 0.5881 (mppt) REVERT: F 24 ASP cc_start: 0.8616 (p0) cc_final: 0.8270 (p0) REVERT: K 2 GLN cc_start: 0.8423 (tp40) cc_final: 0.8209 (tp40) REVERT: K 24 GLU cc_start: 0.9467 (OUTLIER) cc_final: 0.9223 (mp0) REVERT: K 40 GLN cc_start: 0.9039 (mp10) cc_final: 0.8752 (mm-40) REVERT: K 42 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7696 (tpm170) REVERT: K 45 PHE cc_start: 0.7670 (t80) cc_final: 0.7463 (t80) outliers start: 28 outliers final: 17 residues processed: 156 average time/residue: 0.1456 time to fit residues: 30.4000 Evaluate side-chains 156 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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 13 ILE Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 42 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 6.9990 chunk 26 optimal weight: 0.0970 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3413 r_free = 0.3413 target = 0.092171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.062466 restraints weight = 28853.403| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.10 r_work: 0.2667 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 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 = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13498 Z= 0.159 Angle : 0.527 5.662 19466 Z= 0.320 Chirality : 0.033 0.131 2219 Planarity : 0.004 0.043 1463 Dihedral : 29.407 177.219 4114 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.51 % Allowed : 21.74 % Favored : 74.75 % 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 aren not related in a simple way. whole: 2.81 (0.30), residues: 831 helix: 3.42 (0.22), residues: 539 sheet: 0.01 (0.98), residues: 26 loop : -1.49 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 30 TYR 0.010 0.001 TYR K 59 PHE 0.008 0.001 PHE K 4 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00341 (13498) covalent geometry : angle 0.52706 (19466) hydrogen bonds : bond 0.05107 ( 773) hydrogen bonds : angle 2.89572 ( 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 169 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8700 (mttp) REVERT: D 28 LYS cc_start: 0.6043 (OUTLIER) cc_final: 0.5798 (mppt) REVERT: F 24 ASP cc_start: 0.8592 (p0) cc_final: 0.8158 (p0) REVERT: K 24 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9210 (mp0) REVERT: K 42 ARG cc_start: 0.8290 (tpm170) cc_final: 0.7621 (tpm170) REVERT: K 59 TYR cc_start: 0.7109 (m-80) cc_final: 0.6842 (m-80) outliers start: 25 outliers final: 17 residues processed: 160 average time/residue: 0.1433 time to fit residues: 30.8490 Evaluate side-chains 159 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 28 LYS 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 73 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 20 SER Chi-restraints excluded: chain K residue 24 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 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 = 0.3436 r_free = 0.3436 target = 0.092995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.063137 restraints weight = 28787.564| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.05 r_work: 0.2680 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 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 = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13498 Z= 0.159 Angle : 0.530 7.426 19466 Z= 0.320 Chirality : 0.033 0.135 2219 Planarity : 0.004 0.047 1463 Dihedral : 29.412 177.086 4114 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.37 % Allowed : 23.00 % 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 aren not related in a simple way. whole: 2.79 (0.30), residues: 831 helix: 3.43 (0.22), residues: 539 sheet: -0.07 (0.97), residues: 26 loop : -1.53 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 30 TYR 0.008 0.001 TYR K 59 PHE 0.011 0.001 PHE A 78 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00341 (13498) covalent geometry : angle 0.53016 (19466) hydrogen bonds : bond 0.05072 ( 773) hydrogen bonds : angle 2.87425 ( 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 164 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8673 (mttp) REVERT: D 28 LYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5747 (mppt) REVERT: F 24 ASP cc_start: 0.8598 (p0) cc_final: 0.8162 (p0) REVERT: K 24 GLU cc_start: 0.9440 (OUTLIER) cc_final: 0.9216 (mp0) REVERT: K 42 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7534 (tpm170) REVERT: K 59 TYR cc_start: 0.7186 (m-80) cc_final: 0.6956 (m-80) outliers start: 24 outliers final: 19 residues processed: 155 average time/residue: 0.1430 time to fit residues: 29.8929 Evaluate side-chains 162 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 28 LYS 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 73 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 24 GLU Chi-restraints excluded: chain K residue 42 ARG 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: 1.9990 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 102 optimal weight: 30.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.092254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.062281 restraints weight = 28347.494| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.01 r_work: 0.2650 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 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 = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 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 : 0.004 0.036 13498 Z= 0.177 Angle : 0.545 8.152 19466 Z= 0.328 Chirality : 0.034 0.132 2219 Planarity : 0.004 0.042 1463 Dihedral : 29.446 177.113 4114 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.51 % Allowed : 23.00 % Favored : 73.49 % 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 aren not related in a simple way. whole: 2.67 (0.30), residues: 831 helix: 3.34 (0.22), residues: 542 sheet: -0.19 (0.94), residues: 26 loop : -1.63 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 30 TYR 0.007 0.001 TYR E 54 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00389 (13498) covalent geometry : angle 0.54538 (19466) hydrogen bonds : bond 0.05604 ( 773) hydrogen bonds : angle 2.94178 ( 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 160 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8690 (mttp) REVERT: C 62 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8247 (mt) REVERT: D 28 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5744 (mppt) REVERT: E 59 GLU cc_start: 0.7965 (pm20) cc_final: 0.7698 (pm20) REVERT: F 24 ASP cc_start: 0.8581 (p0) cc_final: 0.8151 (p0) REVERT: K 11 LYS cc_start: 0.9303 (tptp) cc_final: 0.9098 (tptp) REVERT: K 24 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.9210 (mp0) REVERT: K 42 ARG cc_start: 0.8251 (tpm170) cc_final: 0.7731 (tpm170) REVERT: K 49 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7801 (mm110) REVERT: K 59 TYR cc_start: 0.7244 (m-80) cc_final: 0.7023 (m-80) outliers start: 25 outliers final: 17 residues processed: 149 average time/residue: 0.1383 time to fit residues: 27.8558 Evaluate side-chains 156 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain D residue 28 LYS 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 73 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 24 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.0570 chunk 9 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3435 r_free = 0.3435 target = 0.093049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.063034 restraints weight = 28522.843| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.06 r_work: 0.2672 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 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 = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13498 Z= 0.151 Angle : 0.537 10.286 19466 Z= 0.323 Chirality : 0.033 0.135 2219 Planarity : 0.004 0.042 1463 Dihedral : 29.450 177.093 4114 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.95 % Allowed : 23.98 % Favored : 73.07 % 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 aren not related in a simple way. whole: 2.72 (0.30), residues: 831 helix: 3.36 (0.22), residues: 543 sheet: -0.20 (0.95), residues: 26 loop : -1.60 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 30 TYR 0.006 0.001 TYR H 37 PHE 0.008 0.001 PHE H 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00312 (13498) covalent geometry : angle 0.53659 (19466) hydrogen bonds : bond 0.05165 ( 773) hydrogen bonds : angle 2.85285 ( 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 162 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8682 (mttp) REVERT: D 28 LYS cc_start: 0.5963 (OUTLIER) cc_final: 0.5722 (mppt) REVERT: E 59 GLU cc_start: 0.7883 (pm20) cc_final: 0.7606 (pm20) REVERT: F 24 ASP cc_start: 0.8591 (p0) cc_final: 0.8099 (p0) REVERT: F 84 MET cc_start: 0.8686 (tpp) cc_final: 0.8452 (mmm) REVERT: K 24 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.9196 (mp0) REVERT: K 42 ARG cc_start: 0.8225 (tpm170) cc_final: 0.7940 (tpm170) REVERT: K 59 TYR cc_start: 0.7228 (m-80) cc_final: 0.6987 (m-80) outliers start: 21 outliers final: 16 residues processed: 154 average time/residue: 0.1389 time to fit residues: 29.2480 Evaluate side-chains 158 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 28 LYS 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 73 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 13 ILE Chi-restraints excluded: chain K residue 24 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3437 r_free = 0.3437 target = 0.093115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.063151 restraints weight = 28810.799| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.04 r_work: 0.2682 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 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 = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13498 Z= 0.155 Angle : 0.541 9.235 19466 Z= 0.324 Chirality : 0.033 0.140 2219 Planarity : 0.004 0.041 1463 Dihedral : 29.432 176.846 4114 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.95 % Allowed : 24.40 % 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 aren not related in a simple way. whole: 2.73 (0.30), residues: 831 helix: 3.40 (0.22), residues: 540 sheet: -0.17 (0.96), residues: 26 loop : -1.60 (0.33), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 30 TYR 0.006 0.001 TYR H 37 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00330 (13498) covalent geometry : angle 0.54052 (19466) hydrogen bonds : bond 0.05058 ( 773) hydrogen bonds : angle 2.85523 ( 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 158 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8668 (mttp) REVERT: D 28 LYS cc_start: 0.5971 (OUTLIER) cc_final: 0.5725 (mppt) REVERT: F 24 ASP cc_start: 0.8541 (p0) cc_final: 0.8046 (p0) REVERT: F 84 MET cc_start: 0.8690 (tpp) cc_final: 0.8463 (mmm) REVERT: K 24 GLU cc_start: 0.9422 (OUTLIER) cc_final: 0.9201 (mp0) REVERT: K 42 ARG cc_start: 0.8279 (tpm170) cc_final: 0.7632 (tpm170) REVERT: K 49 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7718 (mm110) REVERT: K 59 TYR cc_start: 0.7245 (m-80) cc_final: 0.6960 (m-80) outliers start: 21 outliers final: 15 residues processed: 149 average time/residue: 0.1430 time to fit residues: 28.8673 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 : 0.340 ------------------------------------------------------------------------------- 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 28 LYS 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 73 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 24 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.086528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.056185 restraints weight = 28732.243| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 2.09 r_work: 0.2515 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 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 = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 13498 Z= 0.328 Angle : 0.664 9.701 19466 Z= 0.392 Chirality : 0.041 0.145 2219 Planarity : 0.005 0.040 1463 Dihedral : 29.641 177.994 4114 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.23 % Allowed : 24.40 % 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 aren not related in a simple way. whole: 2.07 (0.29), residues: 831 helix: 2.84 (0.22), residues: 542 sheet: -0.22 (0.96), residues: 26 loop : -1.81 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 30 TYR 0.015 0.002 TYR E 54 PHE 0.014 0.002 PHE D 62 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00763 (13498) covalent geometry : angle 0.66432 (19466) hydrogen bonds : bond 0.08614 ( 773) hydrogen bonds : angle 3.48290 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2516.85 seconds wall clock time: 43 minutes 47.67 seconds (2627.67 seconds total)