Starting phenix.real_space_refine on Tue Mar 3 14:10:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r4j_53569/03_2026/9r4j_53569.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r4j_53569/03_2026/9r4j_53569.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/9r4j_53569/03_2026/9r4j_53569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r4j_53569/03_2026/9r4j_53569.map" model { file = "/net/cci-nas-00/data/ceres_data/9r4j_53569/03_2026/9r4j_53569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r4j_53569/03_2026/9r4j_53569.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 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 68 5.49 5 S 12 5.16 5 C 3464 2.51 5 N 1002 2.21 5 O 1242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5788 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1051 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain breaks: 1 Chain: "B" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1134 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "C" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1067 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain breaks: 1 Chain: "A" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1143 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain: "Y" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 688 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "Z" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 705 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Time building chain proxies: 1.40, per 1000 atoms: 0.24 Number of scatterers: 5788 At special positions: 0 Unit cell: (72.171, 114.453, 128.304, 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 12 16.00 P 68 15.00 O 1242 8.00 N 1002 7.00 C 3464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 279.2 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1054 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 40.3% alpha, 20.8% beta 26 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'D' and resid 44 through 55 removed outlier: 3.625A pdb=" N GLU D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.858A pdb=" N LEU D 71 " --> pdb=" O THR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.873A pdb=" N ALA D 76 " --> pdb=" O PHE D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 90 through 95 removed outlier: 4.132A pdb=" N SER D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 129 through 136 removed outlier: 3.680A pdb=" N ARG D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 25 removed outlier: 4.008A pdb=" N SER B 24 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.815A pdb=" N ASN B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 73 Processing helix chain 'B' and resid 90 through 98 removed outlier: 3.793A pdb=" N SER B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'C' and resid 21 through 25 removed outlier: 3.892A pdb=" N SER C 24 " --> pdb=" O LYS C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 64 through 73 removed outlier: 3.581A pdb=" N LYS C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ARG C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.773A pdb=" N SER C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'A' and resid 19 through 24 removed outlier: 4.145A pdb=" N SER A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.650A pdb=" N PHE A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 116 through 126 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.739A pdb=" N ARG A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 9 removed outlier: 4.081A pdb=" N GLY D 4 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 40 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 8 removed outlier: 4.203A pdb=" N GLY B 4 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 9 removed outlier: 3.568A pdb=" N HIS C 111 " --> pdb=" O GLN C 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 30 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 15 through 17 Processing sheet with id=AA7, first strand: chain 'A' and resid 4 through 9 removed outlier: 4.254A pdb=" N GLY A 4 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 16 through 17 194 hydrogen bonds defined for protein. 537 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1012 1.32 - 1.44: 1776 1.44 - 1.56: 3085 1.56 - 1.68: 135 1.68 - 1.80: 20 Bond restraints: 6028 Sorted by residual: bond pdb=" CB GLU D 131 " pdb=" CG GLU D 131 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.43e+00 bond pdb=" O5' DT Y -7 " pdb=" C5' DT Y -7 " ideal model delta sigma weight residual 1.423 1.380 0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" O5' DT Z -4 " pdb=" C5' DT Z -4 " ideal model delta sigma weight residual 1.423 1.384 0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" C ILE B 106 " pdb=" N GLY B 107 " ideal model delta sigma weight residual 1.331 1.322 0.009 6.60e-03 2.30e+04 1.68e+00 bond pdb=" CG GLU D 37 " pdb=" CD GLU D 37 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.51e+00 ... (remaining 6023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 8035 1.91 - 3.81: 343 3.81 - 5.72: 38 5.72 - 7.63: 13 7.63 - 9.53: 2 Bond angle restraints: 8431 Sorted by residual: angle pdb=" CB LYS C 117 " pdb=" CG LYS C 117 " pdb=" CD LYS C 117 " ideal model delta sigma weight residual 111.30 120.83 -9.53 2.30e+00 1.89e-01 1.72e+01 angle pdb=" CA GLU A 113 " pdb=" CB GLU A 113 " pdb=" CG GLU A 113 " ideal model delta sigma weight residual 114.10 121.35 -7.25 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA LYS D 69 " pdb=" CB LYS D 69 " pdb=" CG LYS D 69 " ideal model delta sigma weight residual 114.10 121.27 -7.17 2.00e+00 2.50e-01 1.28e+01 angle pdb=" CA GLU D 131 " pdb=" CB GLU D 131 " pdb=" CG GLU D 131 " ideal model delta sigma weight residual 114.10 121.25 -7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" C THR C 65 " pdb=" N ARG C 66 " pdb=" CA ARG C 66 " ideal model delta sigma weight residual 120.60 126.30 -5.70 1.60e+00 3.91e-01 1.27e+01 ... (remaining 8426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 3056 35.52 - 71.03: 426 71.03 - 106.55: 8 106.55 - 142.06: 2 142.06 - 177.58: 4 Dihedral angle restraints: 3496 sinusoidal: 1897 harmonic: 1599 Sorted by residual: dihedral pdb=" CA GLN B 108 " pdb=" C GLN B 108 " pdb=" N PHE B 109 " pdb=" CA PHE B 109 " ideal model delta harmonic sigma weight residual 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA TRP A 115 " pdb=" C TRP A 115 " pdb=" N ASP A 116 " pdb=" CA ASP A 116 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA ASN B 12 " pdb=" C ASN B 12 " pdb=" N LYS B 13 " pdb=" CA LYS B 13 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 3493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 687 0.051 - 0.102: 218 0.102 - 0.154: 44 0.154 - 0.205: 4 0.205 - 0.256: 7 Chirality restraints: 960 Sorted by residual: chirality pdb=" CB ILE A 42 " pdb=" CA ILE A 42 " pdb=" CG1 ILE A 42 " pdb=" CG2 ILE A 42 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE A 87 " pdb=" CA ILE A 87 " pdb=" CG1 ILE A 87 " pdb=" CG2 ILE A 87 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ASN A 38 " pdb=" N ASN A 38 " pdb=" C ASN A 38 " pdb=" CB ASN A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 957 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG Y -10 " -0.026 2.00e-02 2.50e+03 1.27e-02 4.83e+00 pdb=" N9 DG Y -10 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG Y -10 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DG Y -10 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG Y -10 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG Y -10 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG Y -10 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG Y -10 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG Y -10 " -0.009 2.00e-02 2.50e+03 pdb=" N2 DG Y -10 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DG Y -10 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG Y -10 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT Z 5 " 0.027 2.00e-02 2.50e+03 1.32e-02 4.38e+00 pdb=" N1 DT Z 5 " -0.028 2.00e-02 2.50e+03 pdb=" C2 DT Z 5 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT Z 5 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT Z 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT Z 5 " 0.008 2.00e-02 2.50e+03 pdb=" O4 DT Z 5 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT Z 5 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT Z 5 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT Z 5 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 115 " 0.022 2.00e-02 2.50e+03 1.27e-02 4.01e+00 pdb=" CG TRP D 115 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP D 115 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP D 115 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 115 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 115 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 115 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 115 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 115 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 115 " 0.001 2.00e-02 2.50e+03 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2189 2.89 - 3.39: 5439 3.39 - 3.90: 10176 3.90 - 4.40: 11559 4.40 - 4.90: 17357 Nonbonded interactions: 46720 Sorted by model distance: nonbonded pdb=" N3 DT Y -27 " pdb=" N4 DC Z 28 " model vdw 2.389 2.560 nonbonded pdb=" OD1 ASN C 38 " pdb=" OE1 GLN C 119 " model vdw 2.431 3.040 nonbonded pdb=" N GLU D 131 " pdb=" OE1 GLU D 131 " model vdw 2.436 3.120 nonbonded pdb=" O5' DT Z -4 " pdb=" O4' DT Z -4 " model vdw 2.462 2.432 nonbonded pdb=" O5' DA Z 17 " pdb=" O4' DA Z 17 " model vdw 2.473 2.432 ... (remaining 46715 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 1 through 53 or resid 65 through 137)) selection = (chain 'B' and (resid 1 through 53 or resid 65 through 137)) selection = (chain 'C' and (resid 1 through 53 or resid 65 through 137)) selection = (chain 'D' and (resid 1 through 53 or resid 65 through 137)) } 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: 3.250 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 : 0.007 0.047 6028 Z= 0.298 Angle : 0.890 9.533 8431 Z= 0.496 Chirality : 0.053 0.256 960 Planarity : 0.006 0.044 848 Dihedral : 25.962 177.578 2442 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 8.08 % Allowed : 44.65 % Favored : 47.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.36), residues: 527 helix: -1.37 (0.35), residues: 175 sheet: 0.03 (0.42), residues: 158 loop : -1.28 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 66 TYR 0.018 0.003 TYR D 51 PHE 0.020 0.003 PHE A 36 TRP 0.032 0.005 TRP D 115 HIS 0.006 0.003 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00690 ( 6028) covalent geometry : angle 0.89003 ( 8431) hydrogen bonds : bond 0.15289 ( 258) hydrogen bonds : angle 7.60831 ( 661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7431 (ttp-170) REVERT: B 30 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8015 (pp) REVERT: A 105 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8548 (tt) outliers start: 40 outliers final: 18 residues processed: 174 average time/residue: 0.1065 time to fit residues: 22.6152 Evaluate side-chains 134 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 105 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN B 53 GLN B 57 ASN B 119 GLN A 0 HIS A 57 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.072258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061034 restraints weight = 20759.116| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.11 r_work: 0.3118 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6028 Z= 0.180 Angle : 0.723 7.877 8431 Z= 0.406 Chirality : 0.043 0.199 960 Planarity : 0.005 0.033 848 Dihedral : 26.793 178.134 1377 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 7.88 % Allowed : 31.92 % Favored : 60.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.37), residues: 527 helix: -0.92 (0.35), residues: 190 sheet: -0.02 (0.43), residues: 168 loop : -1.10 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 34 TYR 0.008 0.001 TYR A 51 PHE 0.015 0.001 PHE C 25 TRP 0.017 0.003 TRP A 115 HIS 0.006 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 6028) covalent geometry : angle 0.72316 ( 8431) hydrogen bonds : bond 0.05893 ( 258) hydrogen bonds : angle 6.03282 ( 661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.5837 (tttt) cc_final: 0.5414 (tttt) REVERT: B 30 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8178 (pp) REVERT: B 43 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.7800 (mtt-85) REVERT: B 110 ASP cc_start: 0.9207 (p0) cc_final: 0.8971 (p0) REVERT: B 128 GLU cc_start: 0.8796 (pt0) cc_final: 0.8423 (tt0) REVERT: C 21 LYS cc_start: 0.8382 (mptt) cc_final: 0.8086 (mmmt) REVERT: C 101 LYS cc_start: 0.7794 (tppp) cc_final: 0.7518 (tppt) REVERT: C 102 GLU cc_start: 0.8535 (mp0) cc_final: 0.8270 (mp0) REVERT: C 108 GLN cc_start: 0.8709 (mp10) cc_final: 0.8105 (mp10) outliers start: 39 outliers final: 19 residues processed: 159 average time/residue: 0.0991 time to fit residues: 19.5152 Evaluate side-chains 135 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 105 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.0040 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 0 HIS ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.070660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059351 restraints weight = 20819.800| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.09 r_work: 0.3062 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6028 Z= 0.206 Angle : 0.701 7.286 8431 Z= 0.395 Chirality : 0.043 0.189 960 Planarity : 0.004 0.034 848 Dihedral : 26.778 177.236 1355 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 8.69 % Allowed : 31.52 % Favored : 59.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.38), residues: 527 helix: -0.49 (0.36), residues: 191 sheet: 0.06 (0.44), residues: 163 loop : -1.30 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 136 TYR 0.008 0.001 TYR A 51 PHE 0.013 0.002 PHE B 52 TRP 0.017 0.003 TRP B 115 HIS 0.011 0.002 HIS A 0 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 6028) covalent geometry : angle 0.70135 ( 8431) hydrogen bonds : bond 0.05725 ( 258) hydrogen bonds : angle 5.85244 ( 661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8306 (t0) cc_final: 0.7996 (p0) REVERT: D 21 LYS cc_start: 0.8734 (mptt) cc_final: 0.8459 (tptp) REVERT: D 106 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8084 (mp) REVERT: D 113 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6854 (mm-30) REVERT: D 116 ASP cc_start: 0.7229 (t0) cc_final: 0.6966 (t0) REVERT: B 30 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8263 (pp) REVERT: B 43 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7760 (mtt-85) REVERT: B 110 ASP cc_start: 0.9279 (p0) cc_final: 0.8979 (p0) REVERT: B 128 GLU cc_start: 0.8994 (pt0) cc_final: 0.8724 (pt0) REVERT: C 21 LYS cc_start: 0.8566 (mptt) cc_final: 0.8241 (mmmt) REVERT: C 101 LYS cc_start: 0.7782 (tppp) cc_final: 0.7384 (tppt) REVERT: C 102 GLU cc_start: 0.8546 (mp0) cc_final: 0.8168 (mp0) REVERT: C 108 GLN cc_start: 0.8668 (mp10) cc_final: 0.8181 (mp10) REVERT: A 110 ASP cc_start: 0.9020 (p0) cc_final: 0.8698 (p0) outliers start: 43 outliers final: 25 residues processed: 149 average time/residue: 0.0973 time to fit residues: 18.1196 Evaluate side-chains 138 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 105 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN B 0 HIS C 119 GLN A 0 HIS ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.070569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.059715 restraints weight = 21229.901| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.98 r_work: 0.3107 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6028 Z= 0.218 Angle : 0.709 7.206 8431 Z= 0.398 Chirality : 0.043 0.176 960 Planarity : 0.004 0.035 848 Dihedral : 26.720 175.379 1355 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 8.28 % Allowed : 31.72 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.37), residues: 527 helix: -0.38 (0.36), residues: 193 sheet: 0.42 (0.48), residues: 138 loop : -1.38 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 136 TYR 0.008 0.001 TYR B 51 PHE 0.035 0.002 PHE B 58 TRP 0.016 0.003 TRP B 115 HIS 0.004 0.002 HIS A 0 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 6028) covalent geometry : angle 0.70903 ( 8431) hydrogen bonds : bond 0.05667 ( 258) hydrogen bonds : angle 5.77990 ( 661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8344 (t0) cc_final: 0.8063 (p0) REVERT: D 106 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8143 (mp) REVERT: D 113 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6529 (tp30) REVERT: D 116 ASP cc_start: 0.7426 (t0) cc_final: 0.7152 (t0) REVERT: D 124 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8680 (pp) REVERT: D 133 VAL cc_start: 0.9115 (t) cc_final: 0.8883 (m) REVERT: B 30 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8321 (pp) REVERT: B 43 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.7847 (mtt-85) REVERT: B 110 ASP cc_start: 0.9185 (p0) cc_final: 0.8958 (p0) REVERT: B 121 GLU cc_start: 0.8227 (pp20) cc_final: 0.8027 (pp20) REVERT: B 128 GLU cc_start: 0.8947 (pt0) cc_final: 0.8653 (pt0) REVERT: C 21 LYS cc_start: 0.8543 (mptt) cc_final: 0.8334 (mmmt) REVERT: C 101 LYS cc_start: 0.7946 (tppp) cc_final: 0.7681 (tppt) REVERT: C 102 GLU cc_start: 0.8508 (mp0) cc_final: 0.8176 (mp0) REVERT: C 105 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8347 (tt) REVERT: C 108 GLN cc_start: 0.8715 (mp10) cc_final: 0.8430 (mm110) REVERT: A 33 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8222 (p0) REVERT: A 110 ASP cc_start: 0.8985 (p0) cc_final: 0.8617 (p0) outliers start: 41 outliers final: 21 residues processed: 152 average time/residue: 0.0971 time to fit residues: 18.2618 Evaluate side-chains 141 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 105 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 1 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 0.0670 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.071484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.060291 restraints weight = 20690.812| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.08 r_work: 0.3091 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6028 Z= 0.157 Angle : 0.676 7.081 8431 Z= 0.380 Chirality : 0.041 0.170 960 Planarity : 0.004 0.031 848 Dihedral : 26.630 172.497 1353 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 6.87 % Allowed : 32.32 % Favored : 60.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.37), residues: 527 helix: -0.22 (0.37), residues: 192 sheet: 0.43 (0.48), residues: 136 loop : -1.51 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 136 TYR 0.007 0.001 TYR C 123 PHE 0.011 0.001 PHE C 25 TRP 0.018 0.003 TRP A 115 HIS 0.002 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6028) covalent geometry : angle 0.67602 ( 8431) hydrogen bonds : bond 0.05334 ( 258) hydrogen bonds : angle 5.43489 ( 661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8301 (t0) cc_final: 0.7914 (p0) REVERT: D 106 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8158 (mp) REVERT: D 116 ASP cc_start: 0.7041 (t0) cc_final: 0.6746 (t0) REVERT: D 133 VAL cc_start: 0.9071 (t) cc_final: 0.8802 (m) REVERT: B 30 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8224 (pp) REVERT: B 99 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7782 (mp) REVERT: B 128 GLU cc_start: 0.9028 (pt0) cc_final: 0.8668 (tt0) REVERT: B 135 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6969 (mp0) REVERT: C 21 LYS cc_start: 0.8581 (mptt) cc_final: 0.8310 (mmmt) REVERT: C 43 ARG cc_start: 0.8560 (mtt90) cc_final: 0.8248 (mtt90) REVERT: C 101 LYS cc_start: 0.7767 (tppp) cc_final: 0.7502 (tppt) REVERT: C 102 GLU cc_start: 0.8505 (mp0) cc_final: 0.8136 (mp0) REVERT: C 108 GLN cc_start: 0.8622 (mp10) cc_final: 0.8287 (mm110) REVERT: A 33 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8351 (p0) REVERT: A 106 ILE cc_start: 0.8408 (tp) cc_final: 0.8010 (pt) REVERT: A 110 ASP cc_start: 0.9008 (p0) cc_final: 0.8606 (p0) REVERT: A 121 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8601 (mt-10) outliers start: 34 outliers final: 20 residues processed: 152 average time/residue: 0.0909 time to fit residues: 17.3027 Evaluate side-chains 144 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 105 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.0470 chunk 5 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 overall best weight: 3.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 0 HIS ** A 119 GLN ** 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 = 0.3455 r_free = 0.3455 target = 0.069302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.057807 restraints weight = 21216.156| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.14 r_work: 0.3027 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 6028 Z= 0.249 Angle : 0.724 6.922 8431 Z= 0.405 Chirality : 0.044 0.186 960 Planarity : 0.004 0.034 848 Dihedral : 26.663 173.426 1351 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 7.27 % Allowed : 31.72 % Favored : 61.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.36), residues: 527 helix: -0.12 (0.37), residues: 189 sheet: 0.41 (0.47), residues: 136 loop : -1.50 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 34 TYR 0.010 0.002 TYR C 51 PHE 0.035 0.002 PHE B 58 TRP 0.015 0.003 TRP A 115 HIS 0.004 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 6028) covalent geometry : angle 0.72360 ( 8431) hydrogen bonds : bond 0.05739 ( 258) hydrogen bonds : angle 5.68393 ( 661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.7280 (t0) cc_final: 0.6956 (t0) REVERT: D 133 VAL cc_start: 0.9105 (t) cc_final: 0.8866 (m) REVERT: B 30 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8298 (pp) REVERT: B 43 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7707 (mtt-85) REVERT: B 94 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8264 (tp) REVERT: B 110 ASP cc_start: 0.9269 (p0) cc_final: 0.8793 (p0) REVERT: B 128 GLU cc_start: 0.9090 (pt0) cc_final: 0.8763 (pt0) REVERT: C 21 LYS cc_start: 0.8738 (mptt) cc_final: 0.8434 (mmmt) REVERT: C 101 LYS cc_start: 0.7917 (tppp) cc_final: 0.7656 (tppt) REVERT: C 102 GLU cc_start: 0.8531 (mp0) cc_final: 0.8082 (mp0) REVERT: C 105 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 33 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8489 (p0) REVERT: A 106 ILE cc_start: 0.8409 (tp) cc_final: 0.7901 (pt) REVERT: A 110 ASP cc_start: 0.9146 (p0) cc_final: 0.8763 (p0) outliers start: 36 outliers final: 26 residues processed: 143 average time/residue: 0.0939 time to fit residues: 16.8839 Evaluate side-chains 141 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 105 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.071792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.060444 restraints weight = 21074.202| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.17 r_work: 0.3096 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6028 Z= 0.154 Angle : 0.678 7.030 8431 Z= 0.383 Chirality : 0.041 0.178 960 Planarity : 0.004 0.036 848 Dihedral : 26.512 170.310 1351 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 6.26 % Allowed : 33.13 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.37), residues: 527 helix: 0.00 (0.38), residues: 192 sheet: 0.40 (0.46), residues: 148 loop : -1.58 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 136 TYR 0.008 0.001 TYR C 123 PHE 0.010 0.001 PHE C 48 TRP 0.019 0.003 TRP A 115 HIS 0.002 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6028) covalent geometry : angle 0.67809 ( 8431) hydrogen bonds : bond 0.05236 ( 258) hydrogen bonds : angle 5.35244 ( 661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 ASP cc_start: 0.8184 (t0) cc_final: 0.7854 (p0) REVERT: D 106 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8206 (mp) REVERT: D 113 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6600 (mm-30) REVERT: D 116 ASP cc_start: 0.7030 (t0) cc_final: 0.6677 (t0) REVERT: D 133 VAL cc_start: 0.9074 (t) cc_final: 0.8832 (m) REVERT: B 30 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8222 (pp) REVERT: B 43 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8730 (mtp85) REVERT: B 99 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7684 (mp) REVERT: B 135 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6865 (mp0) REVERT: C 21 LYS cc_start: 0.8663 (mptt) cc_final: 0.8378 (mmmt) REVERT: C 43 ARG cc_start: 0.8524 (mtt90) cc_final: 0.8158 (mtt90) REVERT: C 101 LYS cc_start: 0.7799 (tppp) cc_final: 0.7592 (tppt) REVERT: C 102 GLU cc_start: 0.8505 (mp0) cc_final: 0.8126 (mp0) REVERT: A 33 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8440 (p0) REVERT: A 98 LYS cc_start: 0.9218 (mtmm) cc_final: 0.8928 (mtmm) REVERT: A 106 ILE cc_start: 0.8066 (tp) cc_final: 0.7640 (pt) REVERT: A 110 ASP cc_start: 0.9072 (p0) cc_final: 0.8716 (p0) REVERT: A 113 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 121 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8591 (mt-10) outliers start: 31 outliers final: 23 residues processed: 147 average time/residue: 0.0940 time to fit residues: 16.9903 Evaluate side-chains 146 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 105 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.072865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.062182 restraints weight = 21322.894| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.03 r_work: 0.3184 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6028 Z= 0.158 Angle : 0.692 7.351 8431 Z= 0.388 Chirality : 0.041 0.174 960 Planarity : 0.004 0.042 848 Dihedral : 26.503 169.349 1351 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 6.46 % Allowed : 33.74 % Favored : 59.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.37), residues: 527 helix: 0.09 (0.38), residues: 192 sheet: 0.36 (0.43), residues: 158 loop : -1.79 (0.43), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 136 TYR 0.007 0.001 TYR C 123 PHE 0.035 0.001 PHE B 58 TRP 0.019 0.003 TRP A 115 HIS 0.002 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6028) covalent geometry : angle 0.69229 ( 8431) hydrogen bonds : bond 0.05124 ( 258) hydrogen bonds : angle 5.21676 ( 661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8247 (mp) REVERT: D 133 VAL cc_start: 0.9068 (t) cc_final: 0.8830 (m) REVERT: B 30 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8250 (pp) REVERT: B 43 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8753 (mtp85) REVERT: B 99 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7837 (mp) REVERT: B 128 GLU cc_start: 0.8674 (pt0) cc_final: 0.8390 (tt0) REVERT: C 102 GLU cc_start: 0.8435 (mp0) cc_final: 0.8122 (mp0) REVERT: C 108 GLN cc_start: 0.8449 (mp10) cc_final: 0.8049 (mp10) REVERT: A 106 ILE cc_start: 0.7977 (tp) cc_final: 0.7604 (pt) REVERT: A 110 ASP cc_start: 0.8998 (p0) cc_final: 0.8674 (p0) REVERT: A 121 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8569 (mt-10) outliers start: 32 outliers final: 22 residues processed: 145 average time/residue: 0.0982 time to fit residues: 17.7037 Evaluate side-chains 142 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 50 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.071452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.060773 restraints weight = 21550.035| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.01 r_work: 0.3149 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6028 Z= 0.196 Angle : 0.720 6.951 8431 Z= 0.403 Chirality : 0.043 0.184 960 Planarity : 0.004 0.035 848 Dihedral : 26.475 170.323 1349 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 5.66 % Allowed : 33.94 % Favored : 60.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.37), residues: 527 helix: -0.19 (0.37), residues: 199 sheet: 0.47 (0.45), residues: 157 loop : -1.69 (0.44), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 136 TYR 0.009 0.001 TYR D 51 PHE 0.013 0.001 PHE A 36 TRP 0.013 0.002 TRP B 115 HIS 0.003 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 6028) covalent geometry : angle 0.72034 ( 8431) hydrogen bonds : bond 0.05365 ( 258) hydrogen bonds : angle 5.36771 ( 661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 LYS cc_start: 0.8766 (mptt) cc_final: 0.8447 (mtpt) REVERT: D 106 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8253 (mp) REVERT: D 113 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6638 (mm-30) REVERT: D 133 VAL cc_start: 0.9117 (t) cc_final: 0.8865 (m) REVERT: B 30 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8306 (pp) REVERT: B 43 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.7705 (mtt-85) REVERT: B 99 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7994 (mp) REVERT: B 110 ASP cc_start: 0.9151 (p0) cc_final: 0.8747 (p0) REVERT: C 21 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8276 (tttm) REVERT: C 101 LYS cc_start: 0.7976 (tppt) cc_final: 0.7595 (tptp) REVERT: C 102 GLU cc_start: 0.8496 (mp0) cc_final: 0.8227 (mp0) REVERT: A 63 LYS cc_start: 0.9308 (tppt) cc_final: 0.9083 (tppt) REVERT: A 106 ILE cc_start: 0.8021 (tp) cc_final: 0.7592 (pt) REVERT: A 110 ASP cc_start: 0.9008 (p0) cc_final: 0.8668 (p0) REVERT: A 121 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8596 (mt-10) REVERT: A 137 MET cc_start: 0.8346 (tpt) cc_final: 0.7963 (tpt) outliers start: 28 outliers final: 23 residues processed: 138 average time/residue: 0.0912 time to fit residues: 15.7485 Evaluate side-chains 141 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 50 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.071133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.060415 restraints weight = 21625.163| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.00 r_work: 0.3143 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6028 Z= 0.197 Angle : 0.730 7.009 8431 Z= 0.408 Chirality : 0.043 0.178 960 Planarity : 0.004 0.039 848 Dihedral : 26.442 170.130 1349 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 5.86 % Allowed : 33.74 % Favored : 60.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.36), residues: 527 helix: -0.21 (0.37), residues: 198 sheet: 0.38 (0.45), residues: 148 loop : -1.60 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 136 TYR 0.010 0.001 TYR D 51 PHE 0.031 0.002 PHE B 58 TRP 0.016 0.003 TRP A 115 HIS 0.003 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 6028) covalent geometry : angle 0.72954 ( 8431) hydrogen bonds : bond 0.05295 ( 258) hydrogen bonds : angle 5.36463 ( 661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8195 (mp) REVERT: D 113 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6634 (mm-30) REVERT: D 133 VAL cc_start: 0.9131 (t) cc_final: 0.8878 (m) REVERT: B 30 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8342 (pp) REVERT: B 43 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7760 (mtt-85) REVERT: B 94 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8400 (tp) REVERT: B 99 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7886 (mp) REVERT: B 110 ASP cc_start: 0.9131 (p0) cc_final: 0.8739 (p0) REVERT: C 21 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8367 (tttm) REVERT: C 96 ASP cc_start: 0.8983 (t0) cc_final: 0.8654 (t0) REVERT: C 101 LYS cc_start: 0.7986 (tppt) cc_final: 0.7568 (tptp) REVERT: C 102 GLU cc_start: 0.8481 (mp0) cc_final: 0.8200 (mp0) REVERT: A 106 ILE cc_start: 0.8037 (tp) cc_final: 0.7677 (pt) REVERT: A 110 ASP cc_start: 0.9019 (p0) cc_final: 0.8671 (p0) REVERT: A 121 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8587 (mt-10) REVERT: A 137 MET cc_start: 0.8373 (tpt) cc_final: 0.7961 (tpt) outliers start: 29 outliers final: 24 residues processed: 136 average time/residue: 0.0920 time to fit residues: 15.7023 Evaluate side-chains 141 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 50 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.071404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.060147 restraints weight = 20820.361| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.10 r_work: 0.3091 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6028 Z= 0.173 Angle : 0.724 7.255 8431 Z= 0.403 Chirality : 0.042 0.173 960 Planarity : 0.004 0.037 848 Dihedral : 26.389 168.363 1349 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 6.06 % Allowed : 34.14 % Favored : 59.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.37), residues: 527 helix: -0.21 (0.37), residues: 199 sheet: 0.39 (0.44), residues: 157 loop : -1.85 (0.43), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 136 TYR 0.007 0.001 TYR D 51 PHE 0.010 0.001 PHE B 52 TRP 0.017 0.003 TRP A 115 HIS 0.002 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 6028) covalent geometry : angle 0.72408 ( 8431) hydrogen bonds : bond 0.05183 ( 258) hydrogen bonds : angle 5.31514 ( 661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1494.98 seconds wall clock time: 26 minutes 13.51 seconds (1573.51 seconds total)