Starting phenix.real_space_refine on Wed Feb 4 06:56:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3n_46540/02_2026/9d3n_46540.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3n_46540/02_2026/9d3n_46540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d3n_46540/02_2026/9d3n_46540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3n_46540/02_2026/9d3n_46540.map" model { file = "/net/cci-nas-00/data/ceres_data/9d3n_46540/02_2026/9d3n_46540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3n_46540/02_2026/9d3n_46540.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 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 192 5.49 5 S 14 5.16 5 C 5305 2.51 5 N 1754 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9401 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 732 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "B" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 626 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 695 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 87} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 689 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 726 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 626 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 687 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 87} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 684 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "I" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1974 Classifications: {'DNA': 96} Link IDs: {'rna3p': 95} Chain: "J" Number of atoms: 1962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1962 Classifications: {'DNA': 96} Link IDs: {'rna3p': 95} Time building chain proxies: 2.16, per 1000 atoms: 0.23 Number of scatterers: 9401 At special positions: 0 Unit cell: (116.875, 81.345, 115.94, 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 14 16.00 P 192 15.00 O 2136 8.00 N 1754 7.00 C 5305 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: 0.79 Conformation dependent library (CDL) restraints added in 175.4 milliseconds 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1290 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 75.5% alpha, 2.9% beta 92 base pairs and 161 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.187A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.557A pdb=" N GLU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.601A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.613A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.904A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.550A pdb=" N THR D 122 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 87 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 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.539A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 18 through 22 removed outlier: 3.520A pdb=" N GLY G 22 " --> pdb=" O SER G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.623A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.618A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 84 removed outlier: 3.524A pdb=" N SER H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.578A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 122 removed outlier: 3.695A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR H 115 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL H 118 " --> pdb=" O GLY H 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.036A 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: 6.839A 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: 7.412A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.971A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 370 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 243 hydrogen bonds 486 hydrogen bond angles 0 basepair planarities 92 basepair parallelities 161 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2385 1.34 - 1.46: 2996 1.46 - 1.58: 4158 1.58 - 1.70: 382 1.70 - 1.82: 26 Bond restraints: 9947 Sorted by residual: bond pdb=" CA LYS B 59 " pdb=" C LYS B 59 " ideal model delta sigma weight residual 1.526 1.541 -0.015 1.36e-02 5.41e+03 1.18e+00 bond pdb=" C LEU G 85 " pdb=" N ALA G 86 " ideal model delta sigma weight residual 1.333 1.318 0.015 1.37e-02 5.33e+03 1.13e+00 bond pdb=" C3' DA J -17 " pdb=" O3' DA J -17 " ideal model delta sigma weight residual 1.422 1.453 -0.031 3.00e-02 1.11e+03 1.04e+00 bond pdb=" CG1 ILE C 62 " pdb=" CD1 ILE C 62 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.02e+00 bond pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 1.516 1.531 -0.016 1.59e-02 3.96e+03 9.66e-01 ... (remaining 9942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 13912 1.94 - 3.88: 312 3.88 - 5.82: 18 5.82 - 7.75: 3 7.75 - 9.69: 1 Bond angle restraints: 14246 Sorted by residual: angle pdb=" CA GLY E 132 " pdb=" C GLY E 132 " pdb=" N GLU E 133 " ideal model delta sigma weight residual 117.40 120.57 -3.17 9.60e-01 1.09e+00 1.09e+01 angle pdb=" CA LYS B 59 " pdb=" CB LYS B 59 " pdb=" CG LYS B 59 " ideal model delta sigma weight residual 114.10 120.64 -6.54 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CB MET E 90 " pdb=" CG MET E 90 " pdb=" SD MET E 90 " ideal model delta sigma weight residual 112.70 122.39 -9.69 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CA GLY D 53 " pdb=" C GLY D 53 " pdb=" N ILE D 54 " ideal model delta sigma weight residual 115.27 117.43 -2.16 7.60e-01 1.73e+00 8.06e+00 angle pdb=" CB GLU B 74 " pdb=" CG GLU B 74 " pdb=" CD GLU B 74 " ideal model delta sigma weight residual 112.60 117.17 -4.57 1.70e+00 3.46e-01 7.22e+00 ... (remaining 14241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 4396 34.87 - 69.74: 1033 69.74 - 104.61: 21 104.61 - 139.48: 1 139.48 - 174.35: 1 Dihedral angle restraints: 5452 sinusoidal: 3445 harmonic: 2007 Sorted by residual: dihedral pdb=" CA LYS B 59 " pdb=" C LYS B 59 " pdb=" N VAL B 60 " pdb=" CA VAL B 60 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" C4' DA J -17 " pdb=" C3' DA J -17 " pdb=" O3' DA J -17 " pdb=" P DG J -16 " ideal model delta sinusoidal sigma weight residual -140.00 34.35 -174.35 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU G 63 " pdb=" C LEU G 63 " pdb=" N GLU G 64 " pdb=" CA GLU G 64 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1023 0.028 - 0.056: 415 0.056 - 0.084: 134 0.084 - 0.112: 50 0.112 - 0.140: 9 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1628 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 17 " 0.025 2.00e-02 2.50e+03 1.26e-02 3.97e+00 pdb=" N1 DT I 17 " -0.027 2.00e-02 2.50e+03 pdb=" C2 DT I 17 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 17 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 17 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 17 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 17 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT I 17 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 17 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DT I 17 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 121 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO H 103 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.022 5.00e-02 4.00e+02 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 329 2.70 - 3.25: 8363 3.25 - 3.80: 17638 3.80 - 4.35: 22149 4.35 - 4.90: 32575 Nonbonded interactions: 81054 Sorted by model distance: nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.145 3.040 nonbonded pdb=" OD1 ASP B 85 " pdb=" OH TYR D 83 " model vdw 2.165 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.248 3.120 nonbonded pdb=" O GLU C 64 " pdb=" ND2 ASN C 68 " model vdw 2.254 3.120 nonbonded pdb=" N GLU C 91 " pdb=" OE1 GLU C 91 " model vdw 2.258 3.120 ... (remaining 81049 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 44 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 133)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 18 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 106)) selection = (chain 'G' and resid 18 through 106) } ncs_group { reference = (chain 'D' and resid 36 through 123) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.860 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 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 : 0.003 0.039 9947 Z= 0.169 Angle : 0.653 9.694 14246 Z= 0.406 Chirality : 0.036 0.140 1631 Planarity : 0.004 0.048 1138 Dihedral : 28.299 174.351 4162 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.35 % Allowed : 25.96 % Favored : 73.68 % 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: -0.11 (0.32), residues: 681 helix: 0.54 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -2.01 (0.45), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.022 0.002 TYR C 50 PHE 0.017 0.002 PHE D 65 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9947) covalent geometry : angle 0.65287 (14246) hydrogen bonds : bond 0.11970 ( 613) hydrogen bonds : angle 4.93826 ( 1587) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.215 Fit side-chains REVERT: A 79 LYS cc_start: 0.5179 (tptm) cc_final: 0.3874 (mptm) REVERT: E 90 MET cc_start: 0.7834 (mmp) cc_final: 0.7477 (mmt) REVERT: H 62 MET cc_start: 0.7507 (mtp) cc_final: 0.7198 (mtt) outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 0.6009 time to fit residues: 68.1786 Evaluate side-chains 92 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 27 GLN E 113 HIS F 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.223773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.168129 restraints weight = 11438.758| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.46 r_work: 0.4043 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9947 Z= 0.160 Angle : 0.578 7.299 14246 Z= 0.338 Chirality : 0.036 0.131 1631 Planarity : 0.004 0.044 1138 Dihedral : 30.580 174.117 2834 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.21 % Allowed : 25.44 % Favored : 70.35 % 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: 0.75 (0.33), residues: 681 helix: 1.18 (0.23), residues: 529 sheet: None (None), residues: 0 loop : -1.87 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 42 TYR 0.019 0.002 TYR H 42 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9947) covalent geometry : angle 0.57789 (14246) hydrogen bonds : bond 0.03914 ( 613) hydrogen bonds : angle 3.33993 ( 1587) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.5234 (tptm) cc_final: 0.3757 (mptm) outliers start: 24 outliers final: 8 residues processed: 111 average time/residue: 0.6961 time to fit residues: 81.6617 Evaluate side-chains 102 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 93 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN F 27 GLN G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.223952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.168303 restraints weight = 11404.626| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.46 r_work: 0.4045 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9947 Z= 0.157 Angle : 0.566 6.972 14246 Z= 0.331 Chirality : 0.035 0.126 1631 Planarity : 0.004 0.038 1138 Dihedral : 30.596 173.904 2834 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.21 % Allowed : 27.37 % Favored : 68.42 % 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: 1.08 (0.33), residues: 681 helix: 1.41 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.85 (0.47), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 72 TYR 0.014 0.002 TYR H 40 PHE 0.013 0.002 PHE A 67 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9947) covalent geometry : angle 0.56605 (14246) hydrogen bonds : bond 0.03755 ( 613) hydrogen bonds : angle 3.16999 ( 1587) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: D 121 TYR cc_start: 0.7366 (t80) cc_final: 0.7093 (t80) REVERT: E 73 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6932 (tt0) outliers start: 24 outliers final: 16 residues processed: 107 average time/residue: 0.6356 time to fit residues: 72.2323 Evaluate side-chains 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 68 ASN F 27 GLN G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.223899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.168346 restraints weight = 11454.862| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 1.46 r_work: 0.4038 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9947 Z= 0.163 Angle : 0.563 6.108 14246 Z= 0.329 Chirality : 0.036 0.125 1631 Planarity : 0.004 0.036 1138 Dihedral : 30.608 174.014 2834 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.96 % Allowed : 27.02 % Favored : 67.02 % 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: 1.25 (0.33), residues: 681 helix: 1.52 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.70 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.013 0.002 TYR H 40 PHE 0.011 0.002 PHE H 70 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 9947) covalent geometry : angle 0.56297 (14246) hydrogen bonds : bond 0.03804 ( 613) hydrogen bonds : angle 3.10942 ( 1587) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.7432 (mtm180) cc_final: 0.6844 (ttm110) REVERT: A 82 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8054 (tt) REVERT: D 121 TYR cc_start: 0.7349 (t80) cc_final: 0.7103 (t80) REVERT: E 73 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: E 125 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7474 (mm-40) outliers start: 34 outliers final: 20 residues processed: 112 average time/residue: 0.6403 time to fit residues: 76.2184 Evaluate side-chains 114 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 93 GLN C 24 GLN D 109 HIS F 27 GLN G 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.221284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.164920 restraints weight = 11518.250| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.46 r_work: 0.4002 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9947 Z= 0.201 Angle : 0.608 7.996 14246 Z= 0.349 Chirality : 0.037 0.131 1631 Planarity : 0.004 0.034 1138 Dihedral : 30.767 173.925 2834 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.96 % Allowed : 28.42 % Favored : 65.61 % 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: 0.87 (0.32), residues: 681 helix: 1.29 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.93 (0.45), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 42 TYR 0.013 0.002 TYR A 54 PHE 0.009 0.002 PHE E 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 9947) covalent geometry : angle 0.60784 (14246) hydrogen bonds : bond 0.04295 ( 613) hydrogen bonds : angle 3.26158 ( 1587) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.215 Fit side-chains REVERT: A 65 LEU cc_start: 0.8348 (mt) cc_final: 0.7981 (tt) REVERT: E 73 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: E 90 MET cc_start: 0.7740 (mmp) cc_final: 0.7519 (mmt) REVERT: E 125 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7568 (mm-40) outliers start: 34 outliers final: 19 residues processed: 115 average time/residue: 0.6405 time to fit residues: 78.2847 Evaluate side-chains 113 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 67 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 93 GLN F 27 GLN G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.223580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.168042 restraints weight = 11645.673| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.47 r_work: 0.4021 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9947 Z= 0.154 Angle : 0.570 6.310 14246 Z= 0.332 Chirality : 0.036 0.133 1631 Planarity : 0.004 0.033 1138 Dihedral : 30.728 174.099 2834 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 5.26 % Allowed : 30.18 % Favored : 64.56 % 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: 1.27 (0.33), residues: 681 helix: 1.57 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.73 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 42 TYR 0.012 0.002 TYR H 40 PHE 0.011 0.001 PHE A 67 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9947) covalent geometry : angle 0.56963 (14246) hydrogen bonds : bond 0.03877 ( 613) hydrogen bonds : angle 3.10315 ( 1587) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.326 Fit side-chains REVERT: A 65 LEU cc_start: 0.8364 (mt) cc_final: 0.8004 (tt) REVERT: B 93 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6992 (pp30) REVERT: C 91 GLU cc_start: 0.8067 (pm20) cc_final: 0.7670 (pm20) REVERT: D 121 TYR cc_start: 0.7261 (t80) cc_final: 0.7007 (t80) REVERT: E 73 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6989 (tt0) REVERT: E 125 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7524 (mm-40) outliers start: 30 outliers final: 17 residues processed: 115 average time/residue: 0.6206 time to fit residues: 76.0466 Evaluate side-chains 110 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.219441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.162969 restraints weight = 11519.800| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.44 r_work: 0.3979 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9947 Z= 0.227 Angle : 0.633 8.167 14246 Z= 0.362 Chirality : 0.039 0.146 1631 Planarity : 0.004 0.035 1138 Dihedral : 30.881 174.553 2834 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.96 % Allowed : 29.30 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.58 (0.32), residues: 681 helix: 1.09 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -2.06 (0.45), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 42 TYR 0.014 0.002 TYR A 54 PHE 0.010 0.002 PHE A 104 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 9947) covalent geometry : angle 0.63251 (14246) hydrogen bonds : bond 0.04668 ( 613) hydrogen bonds : angle 3.37550 ( 1587) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.199 Fit side-chains REVERT: A 65 LEU cc_start: 0.8408 (mt) cc_final: 0.8007 (tt) REVERT: C 38 ASN cc_start: 0.7108 (m-40) cc_final: 0.6874 (m-40) REVERT: D 121 TYR cc_start: 0.7266 (t80) cc_final: 0.6964 (t80) REVERT: E 73 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6987 (tt0) REVERT: E 90 MET cc_start: 0.7719 (mmp) cc_final: 0.7423 (mmt) REVERT: E 125 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7546 (mm-40) REVERT: H 49 HIS cc_start: 0.6878 (m-70) cc_final: 0.6634 (m90) REVERT: H 59 MET cc_start: 0.8036 (mmm) cc_final: 0.7704 (mtm) outliers start: 34 outliers final: 19 residues processed: 119 average time/residue: 0.6178 time to fit residues: 78.1380 Evaluate side-chains 114 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 93 GLN F 27 GLN G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.222154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.166755 restraints weight = 11555.608| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 1.44 r_work: 0.4016 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9947 Z= 0.159 Angle : 0.602 7.865 14246 Z= 0.348 Chirality : 0.036 0.133 1631 Planarity : 0.004 0.032 1138 Dihedral : 30.864 174.734 2834 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.21 % Allowed : 32.11 % Favored : 63.68 % 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: 0.94 (0.32), residues: 681 helix: 1.35 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.94 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 39 TYR 0.016 0.002 TYR G 50 PHE 0.012 0.001 PHE A 67 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9947) covalent geometry : angle 0.60199 (14246) hydrogen bonds : bond 0.04138 ( 613) hydrogen bonds : angle 3.21423 ( 1587) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.263 Fit side-chains REVERT: A 65 LEU cc_start: 0.8331 (mt) cc_final: 0.7952 (tt) REVERT: D 121 TYR cc_start: 0.7228 (t80) cc_final: 0.6922 (t80) REVERT: E 73 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: E 90 MET cc_start: 0.7678 (mmp) cc_final: 0.7396 (mmt) REVERT: E 125 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7512 (mm-40) REVERT: H 49 HIS cc_start: 0.6833 (m-70) cc_final: 0.6379 (m170) outliers start: 24 outliers final: 19 residues processed: 113 average time/residue: 0.6037 time to fit residues: 72.6508 Evaluate side-chains 112 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 0.0870 chunk 78 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 93 GLN F 27 GLN G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.223875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.168631 restraints weight = 11524.177| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 1.47 r_work: 0.4040 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9947 Z= 0.146 Angle : 0.581 9.356 14246 Z= 0.338 Chirality : 0.036 0.137 1631 Planarity : 0.004 0.041 1138 Dihedral : 30.776 174.725 2834 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.86 % Allowed : 32.98 % Favored : 63.16 % 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: 1.38 (0.33), residues: 681 helix: 1.64 (0.23), residues: 529 sheet: None (None), residues: 0 loop : -1.71 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 39 TYR 0.013 0.002 TYR H 40 PHE 0.013 0.001 PHE A 67 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9947) covalent geometry : angle 0.58092 (14246) hydrogen bonds : bond 0.03831 ( 613) hydrogen bonds : angle 3.09221 ( 1587) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.266 Fit side-chains REVERT: A 65 LEU cc_start: 0.8309 (mt) cc_final: 0.7950 (tt) REVERT: B 52 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6899 (tp30) REVERT: B 93 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6731 (pp30) REVERT: C 91 GLU cc_start: 0.7933 (mp0) cc_final: 0.7700 (pm20) REVERT: D 121 TYR cc_start: 0.7258 (t80) cc_final: 0.6950 (t80) REVERT: E 73 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6971 (tt0) REVERT: E 125 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7348 (mm110) REVERT: H 49 HIS cc_start: 0.6808 (m-70) cc_final: 0.6290 (m170) outliers start: 22 outliers final: 14 residues processed: 105 average time/residue: 0.6399 time to fit residues: 71.3611 Evaluate side-chains 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 93 GLN F 27 GLN G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.224417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.169201 restraints weight = 11552.515| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.45 r_work: 0.4045 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9947 Z= 0.146 Angle : 0.578 9.393 14246 Z= 0.334 Chirality : 0.035 0.134 1631 Planarity : 0.004 0.055 1138 Dihedral : 30.689 175.040 2834 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.16 % Allowed : 33.68 % Favored : 63.16 % 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: 1.61 (0.33), residues: 681 helix: 1.83 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.75 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 42 TYR 0.012 0.002 TYR H 40 PHE 0.011 0.001 PHE A 67 HIS 0.009 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9947) covalent geometry : angle 0.57820 (14246) hydrogen bonds : bond 0.03711 ( 613) hydrogen bonds : angle 3.02079 ( 1587) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.263 Fit side-chains REVERT: A 65 LEU cc_start: 0.8342 (mt) cc_final: 0.7967 (tt) REVERT: B 52 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6842 (tp30) REVERT: B 92 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6888 (ptm-80) REVERT: B 93 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6751 (pp30) REVERT: C 91 GLU cc_start: 0.7895 (mp0) cc_final: 0.7683 (pm20) REVERT: D 121 TYR cc_start: 0.7258 (t80) cc_final: 0.6942 (t80) REVERT: E 73 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6944 (tt0) REVERT: E 90 MET cc_start: 0.7631 (mmp) cc_final: 0.7327 (mmt) REVERT: H 49 HIS cc_start: 0.6846 (m-70) cc_final: 0.6370 (m170) REVERT: H 52 THR cc_start: 0.8929 (m) cc_final: 0.8479 (p) outliers start: 18 outliers final: 14 residues processed: 107 average time/residue: 0.5623 time to fit residues: 64.0449 Evaluate side-chains 109 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 93 GLN F 27 GLN G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.225185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.170088 restraints weight = 11475.089| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 1.44 r_work: 0.4059 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9947 Z= 0.144 Angle : 0.569 9.159 14246 Z= 0.330 Chirality : 0.035 0.131 1631 Planarity : 0.004 0.033 1138 Dihedral : 30.649 175.097 2834 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.33 % Allowed : 33.86 % Favored : 62.81 % 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: 1.80 (0.33), residues: 681 helix: 2.00 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.63 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 42 TYR 0.012 0.001 TYR H 40 PHE 0.011 0.001 PHE A 67 HIS 0.009 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9947) covalent geometry : angle 0.56873 (14246) hydrogen bonds : bond 0.03643 ( 613) hydrogen bonds : angle 3.00690 ( 1587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.80 seconds wall clock time: 48 minutes 22.67 seconds (2902.67 seconds total)