Starting phenix.real_space_refine on Sat Jan 18 13:56:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v28_42901/01_2025/8v28_42901_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v28_42901/01_2025/8v28_42901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v28_42901/01_2025/8v28_42901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v28_42901/01_2025/8v28_42901.map" model { file = "/net/cci-nas-00/data/ceres_data/8v28_42901/01_2025/8v28_42901_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v28_42901/01_2025/8v28_42901_neut.cif" } resolution = 3.36 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 15 5.16 5 C 7046 2.51 5 N 2380 2.21 5 O 2930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12659 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: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 7.61, per 1000 atoms: 0.60 Number of scatterers: 12659 At special positions: 0 Unit cell: (100.88, 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 15 16.00 P 288 15.00 O 2930 8.00 N 2380 7.00 C 7046 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: 2.89 Conformation dependent library (CDL) restraints added in 978.1 milliseconds 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 67.0% alpha, 4.3% beta 139 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 5.72 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.829A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.772A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.653A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (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: 4.171A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.562A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.631A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.518A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) 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: 3.657A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.645A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.564A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.717A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.520A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) 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: 4.176A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.551A 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: 3.595A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.545A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) 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: 3.576A 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 Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 37 through 41 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A 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: 7.330A 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: 6.738A 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: 7.385A 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 12 through 16 421 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2434 1.33 - 1.45: 4277 1.45 - 1.57: 6155 1.57 - 1.69: 576 1.69 - 1.81: 26 Bond restraints: 13468 Sorted by residual: bond pdb=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.460 1.384 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1' DG J -70 " pdb=" N9 DG J -70 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C1' DA I 72 " pdb=" N9 DA I 72 " ideal model delta sigma weight residual 1.460 1.390 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N TYR B 98 " pdb=" CA TYR B 98 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.21e-02 6.83e+03 5.20e+00 bond pdb=" N ASP H 65 " pdb=" CA ASP H 65 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.20e+00 ... (remaining 13463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19164 2.13 - 4.26: 239 4.26 - 6.39: 17 6.39 - 8.52: 1 8.52 - 10.65: 5 Bond angle restraints: 19426 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 120.20 109.55 10.65 1.50e+00 4.44e-01 5.05e+01 angle pdb=" C3' DC J 70 " pdb=" O3' DC J 70 " pdb=" P DG J 71 " ideal model delta sigma weight residual 120.20 109.76 10.44 1.50e+00 4.44e-01 4.84e+01 angle pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sigma weight residual 120.20 110.58 9.62 1.50e+00 4.44e-01 4.12e+01 angle pdb=" CB ARG K 42 " pdb=" CG ARG K 42 " pdb=" CD ARG K 42 " ideal model delta sigma weight residual 111.30 120.88 -9.58 2.30e+00 1.89e-01 1.73e+01 angle pdb=" CA LYS C 118 " pdb=" CB LYS C 118 " pdb=" CG LYS C 118 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 ... (remaining 19421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 6009 35.66 - 71.32: 1362 71.32 - 106.98: 13 106.98 - 142.65: 4 142.65 - 178.31: 1 Dihedral angle restraints: 7389 sinusoidal: 4936 harmonic: 2453 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 38.31 -178.31 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 91.35 128.65 1 3.50e+01 8.16e-04 1.27e+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 95.57 124.43 1 3.50e+01 8.16e-04 1.23e+01 ... (remaining 7386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2164 0.093 - 0.186: 48 0.186 - 0.279: 0 0.279 - 0.373: 0 0.373 - 0.466: 3 Chirality restraints: 2215 Sorted by residual: chirality pdb=" P DC J 70 " pdb=" OP1 DC J 70 " pdb=" OP2 DC J 70 " pdb=" O5' DC J 70 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.42e+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 -2.80 -0.45 2.00e-01 2.50e+01 5.17e+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 -2.80 -0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 2212 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASP F 24 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.014 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 4.18e+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 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.024 2.00e-02 2.50e+03 1.00e-02 3.01e+00 pdb=" N9 DG I 47 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2842 2.82 - 3.34: 10531 3.34 - 3.86: 22604 3.86 - 4.38: 26544 4.38 - 4.90: 38192 Nonbonded interactions: 100713 Sorted by model distance: nonbonded pdb=" O THR E 58 " pdb=" OG1 THR E 58 " model vdw 2.295 3.040 nonbonded pdb=" O GLN K 2 " pdb=" N GLU K 64 " model vdw 2.347 3.120 nonbonded pdb=" O ARG A 129 " pdb=" NH1 ARG A 129 " model vdw 2.361 3.120 nonbonded pdb=" N ASP F 85 " pdb=" OD1 ASP F 85 " model vdw 2.362 3.120 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.376 3.040 ... (remaining 100708 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 32.740 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 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 0.076 13468 Z= 0.237 Angle : 0.582 10.654 19426 Z= 0.351 Chirality : 0.038 0.466 2215 Planarity : 0.004 0.037 1457 Dihedral : 27.274 178.308 5803 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.56 % Allowed : 19.15 % Favored : 80.28 % 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: 2.83 (0.30), residues: 827 helix: 3.33 (0.22), residues: 530 sheet: 1.37 (1.73), residues: 12 loop : -1.10 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE F 61 TYR 0.017 0.001 TYR H 80 ARG 0.008 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.972 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 114 average time/residue: 0.3708 time to fit residues: 55.1093 Evaluate side-chains 110 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.092165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.060552 restraints weight = 29960.892| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.13 r_work: 0.2649 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 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 0.034 13468 Z= 0.253 Angle : 0.547 7.287 19426 Z= 0.331 Chirality : 0.034 0.133 2215 Planarity : 0.004 0.035 1457 Dihedral : 29.358 178.217 4112 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.55 % Allowed : 19.44 % Favored : 79.01 % 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: 3.03 (0.30), residues: 827 helix: 3.44 (0.22), residues: 531 sheet: 1.27 (1.31), residues: 20 loop : -1.02 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 106 PHE 0.010 0.001 PHE F 61 TYR 0.015 0.001 TYR B 98 ARG 0.004 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.902 Fit side-chains REVERT: A 83 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8380 (mtp180) REVERT: D 73 GLU cc_start: 0.9141 (tp30) cc_final: 0.8826 (tp30) REVERT: E 118 THR cc_start: 0.9470 (m) cc_final: 0.9262 (p) REVERT: F 24 ASP cc_start: 0.8484 (p0) cc_final: 0.8215 (p0) REVERT: H 65 ASP cc_start: 0.8786 (t0) cc_final: 0.8575 (t0) outliers start: 11 outliers final: 5 residues processed: 123 average time/residue: 0.3822 time to fit residues: 60.7854 Evaluate side-chains 114 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 4 optimal weight: 0.0370 chunk 94 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.089356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.057664 restraints weight = 29866.963| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.04 r_work: 0.2582 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13468 Z= 0.350 Angle : 0.600 6.900 19426 Z= 0.360 Chirality : 0.038 0.142 2215 Planarity : 0.005 0.060 1457 Dihedral : 29.632 178.783 4110 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.68 % Allowed : 20.42 % Favored : 76.90 % 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: 827 helix: 3.15 (0.22), residues: 532 sheet: 1.07 (1.35), residues: 20 loop : -1.22 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.013 0.002 PHE D 67 TYR 0.017 0.002 TYR H 39 ARG 0.007 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.948 Fit side-chains REVERT: A 83 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8361 (mtp180) REVERT: C 118 LYS cc_start: 0.8655 (tmtt) cc_final: 0.8403 (tmtt) REVERT: D 73 GLU cc_start: 0.9199 (tp30) cc_final: 0.8842 (tp30) REVERT: E 106 ASP cc_start: 0.8325 (m-30) cc_final: 0.8121 (m-30) REVERT: E 118 THR cc_start: 0.9488 (m) cc_final: 0.9267 (p) REVERT: F 24 ASP cc_start: 0.8598 (p0) cc_final: 0.8343 (p0) REVERT: F 74 GLU cc_start: 0.9085 (tp30) cc_final: 0.8732 (mt-10) REVERT: H 32 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7680 (mm-30) outliers start: 19 outliers final: 12 residues processed: 127 average time/residue: 0.3322 time to fit residues: 56.1781 Evaluate side-chains 125 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 0.0670 chunk 100 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 0.0670 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.094934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.063530 restraints weight = 29812.289| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.12 r_work: 0.2715 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13468 Z= 0.157 Angle : 0.514 5.451 19426 Z= 0.312 Chirality : 0.032 0.126 2215 Planarity : 0.004 0.040 1457 Dihedral : 29.434 178.405 4110 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.83 % Allowed : 20.99 % Favored : 77.18 % 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: 3.17 (0.30), residues: 827 helix: 3.58 (0.22), residues: 531 sheet: 1.74 (1.35), residues: 19 loop : -1.04 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.009 0.001 PHE H 67 TYR 0.008 0.001 TYR H 80 ARG 0.005 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.955 Fit side-chains REVERT: A 83 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8650 (mtp85) REVERT: B 91 LYS cc_start: 0.9367 (tptm) cc_final: 0.9117 (tptm) REVERT: C 118 LYS cc_start: 0.8652 (tmtt) cc_final: 0.8443 (tmtt) REVERT: D 73 GLU cc_start: 0.9218 (tp30) cc_final: 0.8882 (tp30) REVERT: F 24 ASP cc_start: 0.8533 (p0) cc_final: 0.8227 (p0) outliers start: 13 outliers final: 6 residues processed: 132 average time/residue: 0.3253 time to fit residues: 57.5319 Evaluate side-chains 113 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 40 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.094478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.062976 restraints weight = 29889.351| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.10 r_work: 0.2698 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13468 Z= 0.185 Angle : 0.511 5.204 19426 Z= 0.311 Chirality : 0.032 0.128 2215 Planarity : 0.004 0.037 1457 Dihedral : 29.476 178.554 4110 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.69 % Allowed : 22.25 % Favored : 76.06 % 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: 3.23 (0.30), residues: 827 helix: 3.62 (0.22), residues: 532 sheet: 1.67 (1.31), residues: 19 loop : -1.02 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 39 PHE 0.009 0.001 PHE F 61 TYR 0.011 0.001 TYR H 80 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.103 Fit side-chains REVERT: A 59 GLU cc_start: 0.8312 (pm20) cc_final: 0.8053 (pm20) REVERT: A 83 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8688 (mtp85) REVERT: D 73 GLU cc_start: 0.9221 (tp30) cc_final: 0.8876 (tp30) REVERT: F 24 ASP cc_start: 0.8513 (p0) cc_final: 0.8182 (p0) outliers start: 12 outliers final: 9 residues processed: 115 average time/residue: 0.3505 time to fit residues: 53.4229 Evaluate side-chains 116 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 43 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.063380 restraints weight = 30286.291| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.12 r_work: 0.2714 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13468 Z= 0.162 Angle : 0.511 6.906 19426 Z= 0.309 Chirality : 0.032 0.127 2215 Planarity : 0.004 0.036 1457 Dihedral : 29.469 178.475 4110 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.97 % Allowed : 22.82 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.24 (0.30), residues: 827 helix: 3.64 (0.22), residues: 532 sheet: 1.64 (1.30), residues: 19 loop : -1.05 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 75 PHE 0.007 0.001 PHE F 61 TYR 0.013 0.001 TYR H 80 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.921 Fit side-chains REVERT: D 73 GLU cc_start: 0.9215 (tp30) cc_final: 0.8927 (tp30) REVERT: F 24 ASP cc_start: 0.8495 (p0) cc_final: 0.8162 (p0) outliers start: 14 outliers final: 10 residues processed: 117 average time/residue: 0.3325 time to fit residues: 51.7882 Evaluate side-chains 115 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN K 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.091611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.059280 restraints weight = 29668.164| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.09 r_work: 0.2622 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13468 Z= 0.288 Angle : 0.561 7.253 19426 Z= 0.337 Chirality : 0.035 0.135 2215 Planarity : 0.004 0.036 1457 Dihedral : 29.564 178.537 4110 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.25 % Allowed : 22.25 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.93 (0.30), residues: 827 helix: 3.45 (0.22), residues: 534 sheet: 1.77 (1.35), residues: 19 loop : -1.33 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 106 PHE 0.011 0.001 PHE F 61 TYR 0.019 0.001 TYR H 80 ARG 0.009 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.014 Fit side-chains REVERT: A 59 GLU cc_start: 0.8486 (pm20) cc_final: 0.8230 (pm20) REVERT: D 32 GLU cc_start: 0.8552 (mp0) cc_final: 0.8285 (mp0) REVERT: D 73 GLU cc_start: 0.9204 (tp30) cc_final: 0.8871 (tp30) REVERT: E 118 THR cc_start: 0.9485 (m) cc_final: 0.9247 (p) REVERT: F 24 ASP cc_start: 0.8551 (p0) cc_final: 0.8320 (p0) REVERT: H 32 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7545 (mm-30) outliers start: 16 outliers final: 14 residues processed: 119 average time/residue: 0.3225 time to fit residues: 51.3209 Evaluate side-chains 120 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 0.0270 chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 52 optimal weight: 0.0000 chunk 83 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 overall best weight: 0.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.093866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063189 restraints weight = 30158.930| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.01 r_work: 0.2714 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13468 Z= 0.159 Angle : 0.521 8.214 19426 Z= 0.314 Chirality : 0.032 0.128 2215 Planarity : 0.004 0.037 1457 Dihedral : 29.451 178.403 4110 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.69 % Allowed : 22.54 % Favored : 75.77 % 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: 3.17 (0.30), residues: 827 helix: 3.62 (0.22), residues: 532 sheet: 1.81 (1.35), residues: 19 loop : -1.15 (0.34), residues: 276 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 0.013 0.001 TYR D 39 ARG 0.009 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.994 Fit side-chains REVERT: D 73 GLU cc_start: 0.9196 (tp30) cc_final: 0.8933 (tp30) REVERT: F 24 ASP cc_start: 0.8491 (p0) cc_final: 0.8144 (p0) REVERT: F 39 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8875 (mmt90) REVERT: H 65 ASP cc_start: 0.8786 (t0) cc_final: 0.8579 (t0) outliers start: 12 outliers final: 10 residues processed: 119 average time/residue: 0.3450 time to fit residues: 54.6495 Evaluate side-chains 121 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 102 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN K 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.092966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.061072 restraints weight = 29832.157| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.10 r_work: 0.2660 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13468 Z= 0.235 Angle : 0.539 8.475 19426 Z= 0.324 Chirality : 0.034 0.131 2215 Planarity : 0.004 0.036 1457 Dihedral : 29.519 178.415 4110 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.97 % Allowed : 22.39 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.04 (0.30), residues: 827 helix: 3.56 (0.22), residues: 534 sheet: 1.69 (1.33), residues: 19 loop : -1.34 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 106 PHE 0.009 0.001 PHE F 61 TYR 0.018 0.001 TYR H 80 ARG 0.009 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 1.017 Fit side-chains REVERT: D 32 GLU cc_start: 0.8505 (mp0) cc_final: 0.8239 (mp0) REVERT: D 73 GLU cc_start: 0.9204 (tp30) cc_final: 0.8919 (tp30) REVERT: F 24 ASP cc_start: 0.8545 (p0) cc_final: 0.8300 (p0) REVERT: H 65 ASP cc_start: 0.8865 (t0) cc_final: 0.8640 (t0) outliers start: 14 outliers final: 13 residues processed: 117 average time/residue: 0.3443 time to fit residues: 53.3163 Evaluate side-chains 120 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 25 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 71 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.062137 restraints weight = 29583.302| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.08 r_work: 0.2682 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13468 Z= 0.174 Angle : 0.529 9.228 19426 Z= 0.318 Chirality : 0.033 0.128 2215 Planarity : 0.004 0.036 1457 Dihedral : 29.511 178.481 4110 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.55 % Allowed : 22.82 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.10 (0.30), residues: 827 helix: 3.55 (0.22), residues: 536 sheet: 1.56 (1.31), residues: 19 loop : -1.22 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 75 PHE 0.008 0.001 PHE F 61 TYR 0.017 0.001 TYR H 80 ARG 0.008 0.000 ARG D 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1654 Ramachandran restraints generated. 827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.964 Fit side-chains REVERT: D 73 GLU cc_start: 0.9206 (tp30) cc_final: 0.8855 (tp30) REVERT: F 24 ASP cc_start: 0.8529 (p0) cc_final: 0.8285 (p0) REVERT: F 39 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8899 (mmt90) REVERT: H 65 ASP cc_start: 0.8849 (t0) cc_final: 0.8598 (t0) outliers start: 11 outliers final: 9 residues processed: 115 average time/residue: 0.3421 time to fit residues: 52.0886 Evaluate side-chains 118 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 6.9990 chunk 102 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN K 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.092368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.060298 restraints weight = 29638.615| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.07 r_work: 0.2641 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13468 Z= 0.254 Angle : 0.552 9.324 19426 Z= 0.331 Chirality : 0.034 0.133 2215 Planarity : 0.004 0.036 1457 Dihedral : 29.543 178.408 4110 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.11 % Allowed : 22.11 % Favored : 75.77 % 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: 2.95 (0.30), residues: 827 helix: 3.51 (0.22), residues: 533 sheet: 1.55 (1.33), residues: 19 loop : -1.40 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 106 PHE 0.009 0.001 PHE F 61 TYR 0.020 0.001 TYR H 80 ARG 0.009 0.000 ARG D 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5137.57 seconds wall clock time: 91 minutes 43.26 seconds (5503.26 seconds total)