Starting phenix.real_space_refine on Thu May 15 02:09:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pc5_17594/05_2025/8pc5_17594.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pc5_17594/05_2025/8pc5_17594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pc5_17594/05_2025/8pc5_17594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pc5_17594/05_2025/8pc5_17594.map" model { file = "/net/cci-nas-00/data/ceres_data/8pc5_17594/05_2025/8pc5_17594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pc5_17594/05_2025/8pc5_17594.cif" } resolution = 3.02 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= 0.001 sd= 0.014 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 294 5.49 5 S 13 5.16 5 C 7172 2.51 5 N 2399 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12836 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 829 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 8.91, per 1000 atoms: 0.69 Number of scatterers: 12836 At special positions: 0 Unit cell: (102.533, 125.04, 123.373, 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 13 16.00 P 294 15.00 O 2958 8.00 N 2399 7.00 C 7172 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: 3.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1598 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 64.4% alpha, 5.0% beta 146 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 6.28 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.595A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.605A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.817A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.702A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.528A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.599A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.523A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.783A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.548A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.520A 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 45 through 72 removed outlier: 4.399A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.113A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.607A 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 96 through 98 removed outlier: 6.578A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.345A 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: 7.577A 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: 7.363A 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 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53 removed outlier: 3.850A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA K 51 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE K 42 " --> pdb=" O ALA K 51 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 5.42 Time building geometry restraints manager: 4.05 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: 2069 1.33 - 1.45: 4662 1.45 - 1.57: 6333 1.57 - 1.69: 586 1.69 - 1.81: 26 Bond restraints: 13676 Sorted by residual: bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.758 0.057 2.00e-02 2.50e+03 8.17e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.766 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" P DT J -72 " pdb=" OP1 DT J -72 " ideal model delta sigma weight residual 1.480 1.522 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" P DC I 69 " pdb=" OP2 DC I 69 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" P DG J 62 " pdb=" OP1 DG J 62 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.51e+00 ... (remaining 13671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 18671 1.67 - 3.33: 963 3.33 - 5.00: 68 5.00 - 6.66: 17 6.66 - 8.33: 11 Bond angle restraints: 19730 Sorted by residual: angle pdb=" O3' DC I 49 " pdb=" P DA I 50 " pdb=" O5' DA I 50 " ideal model delta sigma weight residual 104.00 95.83 8.17 1.50e+00 4.44e-01 2.97e+01 angle pdb=" C4' DC I 49 " pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 110.00 102.83 7.17 1.50e+00 4.44e-01 2.29e+01 angle pdb=" O3' DA J -73 " pdb=" P DT J -72 " pdb=" O5' DT J -72 " ideal model delta sigma weight residual 104.00 109.54 -5.54 1.50e+00 4.44e-01 1.36e+01 angle pdb=" C3' DA J -73 " pdb=" O3' DA J -73 " pdb=" P DT J -72 " ideal model delta sigma weight residual 120.20 125.37 -5.17 1.50e+00 4.44e-01 1.19e+01 angle pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sigma weight residual 120.20 125.25 -5.05 1.50e+00 4.44e-01 1.13e+01 ... (remaining 19725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 5857 35.94 - 71.87: 1586 71.87 - 107.81: 28 107.81 - 143.75: 3 143.75 - 179.69: 3 Dihedral angle restraints: 7477 sinusoidal: 5003 harmonic: 2474 Sorted by residual: dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual -140.00 39.69 -179.69 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 25.29 -165.29 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DA J -73 " pdb=" C3' DA J -73 " pdb=" O3' DA J -73 " pdb=" P DT J -72 " ideal model delta sinusoidal sigma weight residual -140.00 18.69 -158.69 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 7474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2146 0.113 - 0.226: 73 0.226 - 0.340: 0 0.340 - 0.453: 1 0.453 - 0.566: 9 Chirality restraints: 2229 Sorted by residual: chirality pdb=" P DA J 65 " pdb=" OP1 DA J 65 " pdb=" OP2 DA J 65 " pdb=" O5' DA J 65 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" P DT J 69 " pdb=" OP1 DT J 69 " pdb=" OP2 DT J 69 " pdb=" O5' DT J 69 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" P DG J 64 " pdb=" OP1 DG J 64 " pdb=" OP2 DG J 64 " pdb=" O5' DG J 64 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.56e+00 ... (remaining 2226 not shown) Planarity restraints: 1479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ML3 A 36 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C ML3 A 36 " -0.049 2.00e-02 2.50e+03 pdb=" O ML3 A 36 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 37 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 49 " -0.029 2.00e-02 2.50e+03 1.85e-02 7.74e+00 pdb=" N1 DC I 49 " 0.043 2.00e-02 2.50e+03 pdb=" C2 DC I 49 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC I 49 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 49 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 49 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC I 49 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC I 49 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 49 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.032 2.00e-02 2.50e+03 1.56e-02 7.29e+00 pdb=" N9 DG I 47 " 0.042 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.002 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 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.003 2.00e-02 2.50e+03 ... (remaining 1476 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1385 2.74 - 3.28: 10741 3.28 - 3.82: 25026 3.82 - 4.36: 30240 4.36 - 4.90: 43301 Nonbonded interactions: 110693 Sorted by model distance: nonbonded pdb=" O HIS B 75 " pdb=" NH2 ARG D 89 " model vdw 2.205 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.218 3.040 nonbonded pdb=" NH2 ARG B 35 " pdb=" OH TYR B 51 " model vdw 2.259 3.120 nonbonded pdb=" NE2 GLN C 104 " pdb=" OE2 GLU E 94 " model vdw 2.263 3.120 nonbonded pdb=" O PRO K 60 " pdb=" ND2 ASN K 64 " model vdw 2.277 3.120 ... (remaining 110688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 7.840 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 38.110 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13676 Z= 0.267 Angle : 0.786 8.330 19730 Z= 0.459 Chirality : 0.060 0.566 2229 Planarity : 0.006 0.048 1479 Dihedral : 29.262 179.686 5879 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.42 % Allowed : 11.08 % Favored : 88.50 % 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: 1.05 (0.29), residues: 831 helix: 1.76 (0.22), residues: 541 sheet: -3.81 (0.82), residues: 12 loop : -1.27 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 21 HIS 0.006 0.002 HIS G 31 PHE 0.014 0.002 PHE A 78 TYR 0.010 0.002 TYR H 34 ARG 0.005 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.12744 ( 781) hydrogen bonds : angle 4.25811 ( 1951) covalent geometry : bond 0.00607 (13676) covalent geometry : angle 0.78649 (19730) *********************** 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 154 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: H 84 SER cc_start: 0.8922 (m) cc_final: 0.8721 (t) outliers start: 3 outliers final: 2 residues processed: 153 average time/residue: 0.3699 time to fit residues: 72.8888 Evaluate side-chains 103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN D 46 HIS E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.083853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.055527 restraints weight = 37425.666| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.72 r_work: 0.2791 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13676 Z= 0.194 Angle : 0.588 9.784 19730 Z= 0.354 Chirality : 0.036 0.134 2229 Planarity : 0.004 0.038 1479 Dihedral : 31.118 162.999 4168 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.82 % Allowed : 12.76 % Favored : 85.41 % 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: 1.66 (0.29), residues: 831 helix: 2.12 (0.22), residues: 559 sheet: -2.30 (0.87), residues: 24 loop : -0.94 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 21 HIS 0.003 0.001 HIS E 113 PHE 0.008 0.001 PHE H 62 TYR 0.008 0.001 TYR B 51 ARG 0.004 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 781) hydrogen bonds : angle 2.95239 ( 1951) covalent geometry : bond 0.00433 (13676) covalent geometry : angle 0.58826 (19730) *********************** 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 120 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 52 PHE cc_start: 0.7834 (m-80) cc_final: 0.7523 (m-80) outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 0.3333 time to fit residues: 50.3182 Evaluate side-chains 105 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 90 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.083605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.054419 restraints weight = 38197.655| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.79 r_work: 0.2730 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13676 Z= 0.172 Angle : 0.557 8.659 19730 Z= 0.338 Chirality : 0.035 0.127 2229 Planarity : 0.004 0.040 1479 Dihedral : 30.669 165.738 4167 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.26 % Allowed : 13.88 % Favored : 84.85 % 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: 2.00 (0.29), residues: 831 helix: 2.41 (0.22), residues: 559 sheet: -2.12 (0.93), residues: 24 loop : -0.90 (0.35), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 82 HIS 0.003 0.001 HIS F 18 PHE 0.007 0.001 PHE H 62 TYR 0.008 0.001 TYR F 51 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 781) hydrogen bonds : angle 2.80808 ( 1951) covalent geometry : bond 0.00387 (13676) covalent geometry : angle 0.55713 (19730) *********************** 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 114 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 79 LYS cc_start: 0.9060 (tttt) cc_final: 0.8834 (tttt) REVERT: H 90 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: K 52 PHE cc_start: 0.7881 (m-80) cc_final: 0.7524 (m-80) outliers start: 9 outliers final: 4 residues processed: 109 average time/residue: 0.3133 time to fit residues: 46.2027 Evaluate side-chains 105 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 90 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.083951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.054785 restraints weight = 37933.000| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.78 r_work: 0.2743 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13676 Z= 0.163 Angle : 0.548 8.844 19730 Z= 0.332 Chirality : 0.034 0.128 2229 Planarity : 0.004 0.037 1479 Dihedral : 30.498 169.985 4165 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.68 % Allowed : 13.74 % Favored : 84.57 % 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: 2.21 (0.29), residues: 831 helix: 2.54 (0.22), residues: 561 sheet: -1.51 (0.97), residues: 24 loop : -0.83 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 82 HIS 0.003 0.001 HIS G 31 PHE 0.008 0.001 PHE H 62 TYR 0.009 0.001 TYR K 68 ARG 0.003 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 781) hydrogen bonds : angle 2.72286 ( 1951) covalent geometry : bond 0.00365 (13676) covalent geometry : angle 0.54764 (19730) *********************** 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 117 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: H 90 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: K 52 PHE cc_start: 0.7878 (m-80) cc_final: 0.7521 (m-80) outliers start: 12 outliers final: 5 residues processed: 111 average time/residue: 0.3209 time to fit residues: 48.2367 Evaluate side-chains 103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.0870 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 108 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.082347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.053048 restraints weight = 37957.612| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.77 r_work: 0.2697 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13676 Z= 0.203 Angle : 0.580 9.563 19730 Z= 0.347 Chirality : 0.036 0.127 2229 Planarity : 0.004 0.037 1479 Dihedral : 30.552 171.084 4165 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.96 % Allowed : 13.88 % Favored : 84.15 % 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: 2.10 (0.29), residues: 831 helix: 2.50 (0.22), residues: 560 sheet: -1.48 (0.92), residues: 28 loop : -0.99 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 82 HIS 0.004 0.001 HIS G 31 PHE 0.008 0.001 PHE H 62 TYR 0.010 0.001 TYR B 51 ARG 0.005 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 781) hydrogen bonds : angle 2.80030 ( 1951) covalent geometry : bond 0.00466 (13676) covalent geometry : angle 0.58040 (19730) *********************** 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 112 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.9012 (t0) cc_final: 0.8802 (t0) REVERT: H 90 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: K 78 ASN cc_start: 0.6889 (p0) cc_final: 0.6677 (p0) outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 0.3221 time to fit residues: 46.7299 Evaluate side-chains 105 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 82 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.079983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.050636 restraints weight = 38486.581| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 1.82 r_work: 0.2634 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 13676 Z= 0.309 Angle : 0.646 10.337 19730 Z= 0.381 Chirality : 0.040 0.139 2229 Planarity : 0.005 0.039 1479 Dihedral : 30.742 168.994 4165 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.40 % Allowed : 15.29 % Favored : 83.31 % 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: 1.71 (0.29), residues: 831 helix: 2.18 (0.22), residues: 561 sheet: -1.59 (0.88), residues: 29 loop : -1.06 (0.35), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 82 HIS 0.005 0.001 HIS G 31 PHE 0.013 0.002 PHE K 44 TYR 0.011 0.002 TYR D 118 ARG 0.006 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.05407 ( 781) hydrogen bonds : angle 3.02742 ( 1951) covalent geometry : bond 0.00718 (13676) covalent geometry : angle 0.64588 (19730) *********************** 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 107 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.967 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 103 average time/residue: 0.3232 time to fit residues: 45.1605 Evaluate side-chains 100 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** F 25 ASN ** 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 = 0.3595 r_free = 0.3595 target = 0.081442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.052367 restraints weight = 37977.992| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.77 r_work: 0.2681 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13676 Z= 0.178 Angle : 0.584 9.362 19730 Z= 0.350 Chirality : 0.036 0.139 2229 Planarity : 0.004 0.038 1479 Dihedral : 30.569 169.199 4165 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.26 % Allowed : 15.71 % Favored : 83.03 % 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: 2.08 (0.29), residues: 831 helix: 2.42 (0.22), residues: 558 sheet: -1.28 (0.97), residues: 24 loop : -0.84 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 82 HIS 0.003 0.001 HIS G 31 PHE 0.010 0.001 PHE K 44 TYR 0.010 0.001 TYR D 118 ARG 0.005 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 781) hydrogen bonds : angle 2.86165 ( 1951) covalent geometry : bond 0.00398 (13676) covalent geometry : angle 0.58448 (19730) *********************** 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 103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: D 31 LYS cc_start: 0.9028 (mttm) cc_final: 0.8826 (mtmm) REVERT: F 95 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8928 (mtt-85) REVERT: G 77 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8644 (mtt180) outliers start: 9 outliers final: 4 residues processed: 100 average time/residue: 0.3433 time to fit residues: 45.4332 Evaluate side-chains 98 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 38 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.082259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.053313 restraints weight = 38229.046| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.77 r_work: 0.2707 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13676 Z= 0.172 Angle : 0.566 8.954 19730 Z= 0.340 Chirality : 0.034 0.129 2229 Planarity : 0.004 0.039 1479 Dihedral : 30.342 171.035 4165 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.54 % Allowed : 15.57 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.32 (0.29), residues: 831 helix: 2.60 (0.22), residues: 560 sheet: -1.10 (0.99), residues: 24 loop : -0.75 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 82 HIS 0.003 0.001 HIS F 18 PHE 0.008 0.001 PHE H 62 TYR 0.010 0.001 TYR D 118 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 781) hydrogen bonds : angle 2.74880 ( 1951) covalent geometry : bond 0.00385 (13676) covalent geometry : angle 0.56611 (19730) *********************** 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 105 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: D 31 LYS cc_start: 0.9019 (mttm) cc_final: 0.8817 (mtmm) REVERT: F 95 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8924 (mtt-85) REVERT: G 77 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8659 (mtt180) outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.3413 time to fit residues: 45.8805 Evaluate side-chains 102 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.082357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.053433 restraints weight = 38014.629| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.76 r_work: 0.2710 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13676 Z= 0.168 Angle : 0.565 9.202 19730 Z= 0.339 Chirality : 0.034 0.128 2229 Planarity : 0.004 0.039 1479 Dihedral : 30.335 171.325 4165 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.26 % Allowed : 15.57 % Favored : 83.17 % 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: 2.39 (0.29), residues: 831 helix: 2.63 (0.22), residues: 560 sheet: -1.00 (1.02), residues: 24 loop : -0.69 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 82 HIS 0.004 0.001 HIS F 18 PHE 0.012 0.001 PHE K 44 TYR 0.009 0.001 TYR D 118 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 781) hydrogen bonds : angle 2.73785 ( 1951) covalent geometry : bond 0.00375 (13676) covalent geometry : angle 0.56478 (19730) *********************** 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 103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: F 95 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8931 (mtt-85) outliers start: 9 outliers final: 8 residues processed: 99 average time/residue: 0.3406 time to fit residues: 45.2984 Evaluate side-chains 103 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.082503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.053593 restraints weight = 37850.187| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.76 r_work: 0.2714 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13676 Z= 0.166 Angle : 0.566 9.741 19730 Z= 0.339 Chirality : 0.034 0.128 2229 Planarity : 0.004 0.039 1479 Dihedral : 30.317 171.656 4165 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.12 % Allowed : 15.71 % Favored : 83.17 % 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: 2.43 (0.29), residues: 831 helix: 2.66 (0.22), residues: 560 sheet: -0.98 (1.02), residues: 24 loop : -0.66 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 82 HIS 0.004 0.001 HIS F 18 PHE 0.010 0.001 PHE K 44 TYR 0.009 0.001 TYR D 118 ARG 0.002 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 781) hydrogen bonds : angle 2.72512 ( 1951) covalent geometry : bond 0.00371 (13676) covalent geometry : angle 0.56635 (19730) ********************** 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 101 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: F 95 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8937 (mtt-85) outliers start: 8 outliers final: 6 residues processed: 98 average time/residue: 0.3328 time to fit residues: 43.9586 Evaluate side-chains 100 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 38 ASN Chi-restraints excluded: chain K residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.053549 restraints weight = 37889.406| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.76 r_work: 0.2713 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13676 Z= 0.175 Angle : 0.572 9.776 19730 Z= 0.343 Chirality : 0.034 0.126 2229 Planarity : 0.004 0.039 1479 Dihedral : 30.302 172.501 4165 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.12 % Allowed : 15.71 % Favored : 83.17 % 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: 2.46 (0.29), residues: 831 helix: 2.67 (0.22), residues: 560 sheet: -0.95 (1.02), residues: 24 loop : -0.62 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 82 HIS 0.003 0.001 HIS F 18 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR D 118 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 781) hydrogen bonds : angle 2.72303 ( 1951) covalent geometry : bond 0.00395 (13676) covalent geometry : angle 0.57231 (19730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8094.89 seconds wall clock time: 140 minutes 44.02 seconds (8444.02 seconds total)