Starting phenix.real_space_refine on Wed Jul 30 12:57:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v27_42900/07_2025/8v27_42900_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v27_42900/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v27_42900/07_2025/8v27_42900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v27_42900/07_2025/8v27_42900.map" model { file = "/net/cci-nas-00/data/ceres_data/8v27_42900/07_2025/8v27_42900_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v27_42900/07_2025/8v27_42900_neut.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.61, per 1000 atoms: 0.60 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: 2.86 Conformation dependent library (CDL) restraints added in 982.0 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: 6.23 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: 5.00 Time building geometry restraints manager: 3.35 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: 1.000 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.300 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.001 HIS F 75 PHE 0.024 0.001 PHE K 4 TYR 0.011 0.001 TYR K 59 ARG 0.009 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.11782 ( 773) hydrogen bonds : angle 3.66615 ( 1944) covalent geometry : bond 0.00370 (13498) covalent geometry : angle 0.59198 (19466) *********************** 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 : 0.912 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: 0.3218 time to fit residues: 59.7484 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 : 0.909 ------------------------------------------------------------------------------- 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 91 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.0050 chunk 98 optimal weight: 6.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.092210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.062622 restraints weight = 28657.433| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.08 r_work: 0.2669 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- 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 = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.0675 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 : 0.536 6.047 19466 Z= 0.326 Chirality : 0.033 0.167 2219 Planarity : 0.004 0.036 1463 Dihedral : 29.250 177.412 4121 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.95 % Allowed : 19.21 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.30), residues: 831 helix: 3.30 (0.22), residues: 539 sheet: 0.38 (1.07), residues: 26 loop : -1.21 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 82 PHE 0.009 0.001 PHE F 61 TYR 0.010 0.001 TYR K 59 ARG 0.003 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.05414 ( 773) hydrogen bonds : angle 3.05508 ( 1944) covalent geometry : bond 0.00355 (13498) covalent geometry : angle 0.53631 (19466) *********************** 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 165 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8670 (mttp) REVERT: F 24 ASP cc_start: 0.8593 (p0) cc_final: 0.8266 (p0) REVERT: F 84 MET cc_start: 0.8617 (tpp) cc_final: 0.8264 (mmm) REVERT: K 24 GLU cc_start: 0.9476 (OUTLIER) cc_final: 0.9203 (mp0) outliers start: 21 outliers final: 12 residues processed: 157 average time/residue: 0.3248 time to fit residues: 67.6573 Evaluate side-chains 150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 D residue 119 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 Chi-restraints excluded: chain K residue 24 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.089542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.059539 restraints weight = 28772.097| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.08 r_work: 0.2595 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1089 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= 0.213 Angle : 0.566 5.801 19466 Z= 0.342 Chirality : 0.035 0.140 2219 Planarity : 0.004 0.035 1463 Dihedral : 29.379 177.774 4114 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.09 % Allowed : 20.34 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.30), residues: 831 helix: 3.17 (0.22), residues: 541 sheet: 0.81 (1.10), residues: 26 loop : -1.41 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 68 PHE 0.011 0.002 PHE K 4 TYR 0.010 0.001 TYR E 54 ARG 0.005 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.06649 ( 773) hydrogen bonds : angle 3.17907 ( 1944) covalent geometry : bond 0.00478 (13498) covalent geometry : angle 0.56565 (19466) *********************** 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 161 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8688 (mttp) REVERT: C 62 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8527 (mt) REVERT: F 24 ASP cc_start: 0.8635 (p0) cc_final: 0.8278 (p0) REVERT: K 40 GLN cc_start: 0.9082 (mp10) cc_final: 0.8766 (mm-40) REVERT: K 42 ARG cc_start: 0.8191 (tpm170) cc_final: 0.7645 (tpm170) REVERT: K 51 GLU cc_start: 0.7769 (tm-30) cc_final: 0.6957 (pm20) outliers start: 22 outliers final: 15 residues processed: 153 average time/residue: 0.3359 time to fit residues: 68.7510 Evaluate side-chains 155 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 92 GLU 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 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 48 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3411 r_free = 0.3411 target = 0.092124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.062584 restraints weight = 28801.229| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.09 r_work: 0.2660 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1068 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= 0.151 Angle : 0.535 7.518 19466 Z= 0.324 Chirality : 0.033 0.133 2219 Planarity : 0.004 0.039 1463 Dihedral : 29.347 177.122 4114 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.23 % Allowed : 21.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.30), residues: 831 helix: 3.34 (0.22), residues: 539 sheet: 0.79 (1.12), residues: 26 loop : -1.35 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.007 0.001 PHE F 61 TYR 0.006 0.001 TYR H 37 ARG 0.021 0.000 ARG K 42 Details of bonding type rmsd hydrogen bonds : bond 0.05295 ( 773) hydrogen bonds : angle 2.94232 ( 1944) covalent geometry : bond 0.00311 (13498) covalent geometry : angle 0.53542 (19466) *********************** 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 166 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8696 (mttp) REVERT: C 42 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7945 (ptp-170) REVERT: F 24 ASP cc_start: 0.8619 (p0) cc_final: 0.8221 (p0) REVERT: G 81 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.9076 (tpt170) REVERT: K 24 GLU cc_start: 0.9458 (OUTLIER) cc_final: 0.9184 (mp0) REVERT: K 42 ARG cc_start: 0.8279 (tpm170) cc_final: 0.7501 (tpm170) REVERT: K 51 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7033 (pm20) outliers start: 23 outliers final: 11 residues processed: 159 average time/residue: 0.3310 time to fit residues: 70.0475 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 : 0.975 ------------------------------------------------------------------------------- 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 42 ARG 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 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 24 GLU Chi-restraints excluded: chain K residue 43 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 50.0000 chunk 48 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.090459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.060589 restraints weight = 28690.375| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.10 r_work: 0.2618 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1229 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= 0.187 Angle : 0.553 7.295 19466 Z= 0.334 Chirality : 0.035 0.146 2219 Planarity : 0.004 0.039 1463 Dihedral : 29.438 177.712 4114 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.23 % Allowed : 21.74 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.30), residues: 831 helix: 3.25 (0.22), residues: 542 sheet: 0.35 (1.05), residues: 26 loop : -1.56 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.011 0.002 PHE A 78 TYR 0.011 0.001 TYR K 59 ARG 0.005 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.06016 ( 773) hydrogen bonds : angle 3.05387 ( 1944) covalent geometry : bond 0.00414 (13498) covalent geometry : angle 0.55293 (19466) *********************** 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 161 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.9103 (t0) cc_final: 0.8817 (t0) REVERT: B 79 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8716 (mttp) REVERT: C 42 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8144 (ptp-170) REVERT: C 62 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8404 (mt) REVERT: F 24 ASP cc_start: 0.8633 (p0) cc_final: 0.8262 (p0) REVERT: K 24 GLU cc_start: 0.9467 (OUTLIER) cc_final: 0.9201 (mp0) REVERT: K 40 GLN cc_start: 0.9003 (mp10) cc_final: 0.8614 (mm-40) outliers start: 23 outliers final: 14 residues processed: 150 average time/residue: 0.3670 time to fit residues: 73.5193 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 : 0.975 ------------------------------------------------------------------------------- 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 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 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 95 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.090213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.060379 restraints weight = 29150.145| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.10 r_work: 0.2605 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-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: 2 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13498 Z= 0.195 Angle : 0.556 5.912 19466 Z= 0.336 Chirality : 0.035 0.138 2219 Planarity : 0.004 0.040 1463 Dihedral : 29.466 177.223 4114 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.93 % Allowed : 22.30 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.30), residues: 831 helix: 3.24 (0.22), residues: 541 sheet: 0.06 (1.00), residues: 26 loop : -1.64 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.010 0.002 PHE F 61 TYR 0.009 0.001 TYR E 54 ARG 0.008 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.06186 ( 773) hydrogen bonds : angle 3.06534 ( 1944) covalent geometry : bond 0.00434 (13498) covalent geometry : angle 0.55567 (19466) *********************** 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: 28 poor density : 138 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8707 (mttp) REVERT: C 42 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8232 (ptp-170) REVERT: F 24 ASP cc_start: 0.8639 (p0) cc_final: 0.8220 (p0) REVERT: F 25 ASN cc_start: 0.9163 (m-40) cc_final: 0.8912 (m110) REVERT: K 2 GLN cc_start: 0.8521 (tp40) cc_final: 0.8258 (tp40) REVERT: K 24 GLU cc_start: 0.9407 (OUTLIER) cc_final: 0.9162 (mp0) REVERT: K 40 GLN cc_start: 0.8993 (mp10) cc_final: 0.8634 (mm-40) REVERT: K 42 ARG cc_start: 0.7991 (tpm170) cc_final: 0.7684 (tpm170) REVERT: K 51 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6713 (pm20) outliers start: 28 outliers final: 18 residues processed: 154 average time/residue: 0.3305 time to fit residues: 67.9036 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 : 0.903 ------------------------------------------------------------------------------- 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 92 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.090648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.060951 restraints weight = 28647.692| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.09 r_work: 0.2618 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 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 = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13498 Z= 0.169 Angle : 0.552 8.172 19466 Z= 0.333 Chirality : 0.034 0.186 2219 Planarity : 0.004 0.041 1463 Dihedral : 29.472 177.310 4114 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.23 % Allowed : 23.84 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.30), residues: 831 helix: 3.26 (0.22), residues: 542 sheet: -0.01 (1.00), residues: 26 loop : -1.61 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE K 4 TYR 0.007 0.001 TYR H 37 ARG 0.008 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.05906 ( 773) hydrogen bonds : angle 3.00815 ( 1944) covalent geometry : bond 0.00368 (13498) covalent geometry : angle 0.55183 (19466) *********************** 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 : 0.919 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.9071 (t0) cc_final: 0.8694 (t0) REVERT: B 79 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8723 (mttp) REVERT: C 42 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7911 (ptp-170) REVERT: C 62 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8326 (mt) REVERT: F 24 ASP cc_start: 0.8627 (p0) cc_final: 0.8206 (p0) REVERT: F 25 ASN cc_start: 0.9155 (m-40) cc_final: 0.8906 (m110) REVERT: K 24 GLU cc_start: 0.9404 (OUTLIER) cc_final: 0.9157 (mp0) REVERT: K 40 GLN cc_start: 0.8972 (mp10) cc_final: 0.8606 (mm-40) REVERT: K 42 ARG cc_start: 0.8085 (tpm170) cc_final: 0.7659 (tpm170) REVERT: K 49 GLN cc_start: 0.8134 (mm110) cc_final: 0.7903 (mm110) REVERT: K 51 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6715 (pm20) outliers start: 23 outliers final: 17 residues processed: 152 average time/residue: 0.3209 time to fit residues: 65.0094 Evaluate side-chains 161 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.090953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.061282 restraints weight = 29072.316| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.09 r_work: 0.2628 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 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 = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13498 Z= 0.169 Angle : 0.551 9.407 19466 Z= 0.331 Chirality : 0.034 0.164 2219 Planarity : 0.004 0.043 1463 Dihedral : 29.464 177.217 4114 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.23 % Allowed : 24.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.30), residues: 831 helix: 3.28 (0.22), residues: 542 sheet: -0.04 (0.99), residues: 26 loop : -1.62 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE F 61 TYR 0.006 0.001 TYR E 54 ARG 0.009 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.05704 ( 773) hydrogen bonds : angle 2.98296 ( 1944) covalent geometry : bond 0.00366 (13498) covalent geometry : angle 0.55089 (19466) *********************** 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 164 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8714 (mttp) REVERT: C 42 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7903 (ptp-170) REVERT: C 62 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8304 (mt) REVERT: F 24 ASP cc_start: 0.8627 (p0) cc_final: 0.8207 (p0) REVERT: K 24 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.9155 (mp0) REVERT: K 42 ARG cc_start: 0.8057 (tpm170) cc_final: 0.7564 (tpm170) REVERT: K 49 GLN cc_start: 0.8036 (mm110) cc_final: 0.7802 (mm-40) REVERT: K 51 GLU cc_start: 0.7353 (tm-30) cc_final: 0.6751 (pm20) outliers start: 23 outliers final: 18 residues processed: 154 average time/residue: 0.3250 time to fit residues: 66.5582 Evaluate side-chains 160 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 92 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 83 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.092073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.062037 restraints weight = 28612.668| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.03 r_work: 0.2649 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 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 = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13498 Z= 0.162 Angle : 0.549 9.585 19466 Z= 0.330 Chirality : 0.034 0.170 2219 Planarity : 0.004 0.043 1463 Dihedral : 29.462 177.213 4114 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.95 % Allowed : 24.96 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.30), residues: 831 helix: 3.30 (0.22), residues: 542 sheet: -0.13 (0.99), residues: 26 loop : -1.62 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.012 0.001 PHE K 4 TYR 0.006 0.001 TYR H 37 ARG 0.008 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.05474 ( 773) hydrogen bonds : angle 2.94794 ( 1944) covalent geometry : bond 0.00346 (13498) covalent geometry : angle 0.54939 (19466) *********************** 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 158 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.9040 (t0) cc_final: 0.8716 (t0) REVERT: B 79 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8692 (mttp) REVERT: C 42 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7817 (ptp-170) REVERT: C 62 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8222 (mt) REVERT: F 24 ASP cc_start: 0.8622 (p0) cc_final: 0.8191 (p0) REVERT: G 84 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.7593 (tp40) REVERT: K 24 GLU cc_start: 0.9404 (OUTLIER) cc_final: 0.9127 (mp0) REVERT: K 42 ARG cc_start: 0.8054 (tpm170) cc_final: 0.7700 (tpm170) REVERT: K 51 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6740 (pm20) outliers start: 21 outliers final: 16 residues processed: 151 average time/residue: 0.3144 time to fit residues: 63.6052 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 : 0.979 ------------------------------------------------------------------------------- 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 42 ARG Chi-restraints excluded: chain C residue 62 ILE 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 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 84 GLN 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 Chi-restraints excluded: chain K residue 20 SER 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 55 optimal weight: 0.0020 chunk 102 optimal weight: 40.0000 chunk 30 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.091646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.061617 restraints weight = 28497.109| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.02 r_work: 0.2638 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 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 = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13498 Z= 0.178 Angle : 0.553 9.209 19466 Z= 0.332 Chirality : 0.034 0.170 2219 Planarity : 0.004 0.043 1463 Dihedral : 29.491 177.442 4114 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.09 % Allowed : 24.82 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.30), residues: 831 helix: 3.29 (0.22), residues: 542 sheet: -0.18 (0.97), residues: 26 loop : -1.68 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE K 45 TYR 0.007 0.001 TYR E 54 ARG 0.008 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.05738 ( 773) hydrogen bonds : angle 2.98607 ( 1944) covalent geometry : bond 0.00391 (13498) covalent geometry : angle 0.55338 (19466) ********************** 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 159 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8692 (mttp) REVERT: C 42 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7929 (ptp-170) REVERT: C 62 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8292 (mt) REVERT: F 24 ASP cc_start: 0.8541 (p0) cc_final: 0.8053 (p0) REVERT: F 84 MET cc_start: 0.8723 (tpp) cc_final: 0.8513 (mmm) REVERT: G 84 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.7613 (tp40) REVERT: K 24 GLU cc_start: 0.9406 (OUTLIER) cc_final: 0.9138 (mp0) REVERT: K 42 ARG cc_start: 0.8032 (tpm170) cc_final: 0.7599 (tpm170) outliers start: 22 outliers final: 16 residues processed: 149 average time/residue: 0.3266 time to fit residues: 64.9373 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 : 0.926 ------------------------------------------------------------------------------- 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 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 118 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 84 GLN 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 20 SER 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 81 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3421 r_free = 0.3421 target = 0.092188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.062097 restraints weight = 28644.603| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.04 r_work: 0.2654 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 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 = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13498 Z= 0.155 Angle : 0.554 9.266 19466 Z= 0.332 Chirality : 0.034 0.138 2219 Planarity : 0.004 0.043 1463 Dihedral : 29.496 177.470 4114 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.81 % Allowed : 25.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.30), residues: 831 helix: 3.32 (0.22), residues: 542 sheet: -0.20 (0.93), residues: 26 loop : -1.66 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.012 0.001 PHE A 78 TYR 0.007 0.001 TYR H 37 ARG 0.009 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.05410 ( 773) hydrogen bonds : angle 2.91526 ( 1944) covalent geometry : bond 0.00326 (13498) covalent geometry : angle 0.55374 (19466) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5393.43 seconds wall clock time: 94 minutes 7.21 seconds (5647.21 seconds total)