Starting phenix.real_space_refine on Fri Jul 3 02:48:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x3x_32996/07_2026/7x3x_32996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x3x_32996/07_2026/7x3x_32996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x3x_32996/07_2026/7x3x_32996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x3x_32996/07_2026/7x3x_32996.map" model { file = "/net/cci-nas-00/data/ceres_data/7x3x_32996/07_2026/7x3x_32996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x3x_32996/07_2026/7x3x_32996.cif" } resolution = 3.2 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= 0.002 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 292 5.49 5 S 12 5.16 5 C 6647 2.51 5 N 2257 2.21 5 O 2828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12036 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} 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: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2978 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3008 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "V" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Time building chain proxies: 2.52, per 1000 atoms: 0.21 Number of scatterers: 12036 At special positions: 0 Unit cell: (93.095, 125.57, 116.91, 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 292 15.00 O 2828 8.00 N 2257 7.00 C 6647 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: 0.88 Conformation dependent library (CDL) restraints added in 217.9 milliseconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 70.9% alpha, 2.6% beta 137 base pairs and 225 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.754A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.969A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.810A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.485A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (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 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.686A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.802A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.422A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.603A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.706A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.886A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.123A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.991A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.547A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 406 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 702 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 225 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.27: 1258 1.27 - 1.41: 3834 1.41 - 1.55: 7099 1.55 - 1.69: 624 1.69 - 1.83: 28 Bond restraints: 12843 Sorted by residual: bond pdb=" C3' DA I 90 " pdb=" O3' DA I 90 " ideal model delta sigma weight residual 1.435 1.823 -0.388 1.30e-02 5.92e+03 8.89e+02 bond pdb=" C1' DT I 87 " pdb=" N1 DT I 87 " ideal model delta sigma weight residual 1.468 1.830 -0.362 1.40e-02 5.10e+03 6.68e+02 bond pdb=" C1' DT I 89 " pdb=" N1 DT I 89 " ideal model delta sigma weight residual 1.468 1.125 0.343 1.40e-02 5.10e+03 6.01e+02 bond pdb=" N7 DG J 55 " pdb=" C5 DG J 55 " ideal model delta sigma weight residual 1.388 1.254 0.134 6.00e-03 2.78e+04 4.96e+02 bond pdb=" N9 DG J 55 " pdb=" C8 DG J 55 " ideal model delta sigma weight residual 1.374 1.239 0.135 7.00e-03 2.04e+04 3.71e+02 ... (remaining 12838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 18456 4.17 - 8.35: 110 8.35 - 12.52: 32 12.52 - 16.69: 7 16.69 - 20.87: 5 Bond angle restraints: 18610 Sorted by residual: angle pdb=" O4' DT I 88 " pdb=" C1' DT I 88 " pdb=" N1 DT I 88 " ideal model delta sigma weight residual 108.00 121.03 -13.03 7.00e-01 2.04e+00 3.46e+02 angle pdb=" O5' DG J 53 " pdb=" C5' DG J 53 " pdb=" C4' DG J 53 " ideal model delta sigma weight residual 109.40 121.17 -11.77 8.00e-01 1.56e+00 2.16e+02 angle pdb=" O5' DA I 91 " pdb=" C5' DA I 91 " pdb=" C4' DA I 91 " ideal model delta sigma weight residual 109.40 120.89 -11.49 8.00e-01 1.56e+00 2.06e+02 angle pdb=" O4' DA I 91 " pdb=" C4' DA I 91 " pdb=" C3' DA I 91 " ideal model delta sigma weight residual 106.00 98.03 7.97 6.00e-01 2.78e+00 1.76e+02 angle pdb=" O5' DG J 56 " pdb=" C5' DG J 56 " pdb=" C4' DG J 56 " ideal model delta sigma weight residual 109.40 119.68 -10.28 8.00e-01 1.56e+00 1.65e+02 ... (remaining 18605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 5604 35.19 - 70.37: 1333 70.37 - 105.56: 27 105.56 - 140.74: 1 140.74 - 175.92: 2 Dihedral angle restraints: 6967 sinusoidal: 4733 harmonic: 2234 Sorted by residual: dihedral pdb=" CA LYS B 20 " pdb=" C LYS B 20 " pdb=" N VAL B 21 " pdb=" CA VAL B 21 " ideal model delta harmonic sigma weight residual 180.00 141.00 39.00 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA ARG B 19 " pdb=" C ARG B 19 " pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta harmonic sigma weight residual -180.00 -153.89 -26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 44.08 175.92 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 6964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2083 0.156 - 0.313: 31 0.313 - 0.469: 7 0.469 - 0.626: 3 0.626 - 0.782: 3 Chirality restraints: 2127 Sorted by residual: chirality pdb=" P DT I 89 " pdb=" OP1 DT I 89 " pdb=" OP2 DT I 89 " pdb=" O5' DT I 89 " both_signs ideal model delta sigma weight residual True 2.34 -1.55 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" C1' DA I 90 " pdb=" O4' DA I 90 " pdb=" C2' DA I 90 " pdb=" N9 DA I 90 " both_signs ideal model delta sigma weight residual False 2.43 1.77 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1' DT I 89 " pdb=" O4' DT I 89 " pdb=" C2' DT I 89 " pdb=" N1 DT I 89 " both_signs ideal model delta sigma weight residual False 2.43 1.79 0.64 2.00e-01 2.50e+01 1.04e+01 ... (remaining 2124 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 55 " 0.071 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" N9 DG J 55 " -0.203 2.00e-02 2.50e+03 pdb=" C8 DG J 55 " 0.030 2.00e-02 2.50e+03 pdb=" N7 DG J 55 " 0.065 2.00e-02 2.50e+03 pdb=" C5 DG J 55 " 0.012 2.00e-02 2.50e+03 pdb=" C6 DG J 55 " 0.035 2.00e-02 2.50e+03 pdb=" O6 DG J 55 " -0.053 2.00e-02 2.50e+03 pdb=" N1 DG J 55 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG J 55 " 0.008 2.00e-02 2.50e+03 pdb=" N2 DG J 55 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DG J 55 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG J 55 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 54 " 0.074 2.00e-02 2.50e+03 4.96e-02 5.54e+01 pdb=" N1 DC J 54 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DC J 54 " -0.062 2.00e-02 2.50e+03 pdb=" O2 DC J 54 " 0.033 2.00e-02 2.50e+03 pdb=" N3 DC J 54 " -0.026 2.00e-02 2.50e+03 pdb=" C4 DC J 54 " -0.052 2.00e-02 2.50e+03 pdb=" N4 DC J 54 " 0.081 2.00e-02 2.50e+03 pdb=" C5 DC J 54 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DC J 54 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 89 " 0.064 2.00e-02 2.50e+03 4.21e-02 4.43e+01 pdb=" N1 DT I 89 " -0.102 2.00e-02 2.50e+03 pdb=" C2 DT I 89 " 0.048 2.00e-02 2.50e+03 pdb=" O2 DT I 89 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DT I 89 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DT I 89 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT I 89 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DT I 89 " 0.016 2.00e-02 2.50e+03 pdb=" C7 DT I 89 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 89 " -0.015 2.00e-02 2.50e+03 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 40 2.54 - 3.13: 8386 3.13 - 3.72: 21654 3.72 - 4.31: 28955 4.31 - 4.90: 42283 Nonbonded interactions: 101318 Sorted by model distance: nonbonded pdb=" O5' DA I 90 " pdb=" O4' DA I 90 " model vdw 1.947 2.432 nonbonded pdb=" O4' DT I 89 " pdb=" C2 DT I 89 " model vdw 2.120 2.608 nonbonded pdb=" C1' DT I 89 " pdb=" O2 DT I 89 " model vdw 2.194 2.776 nonbonded pdb=" OE2 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.206 3.120 nonbonded pdb=" O4' DT I 89 " pdb=" O2 DT I 89 " model vdw 2.206 3.040 ... (remaining 101313 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 19 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 19 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.960 Find NCS groups from input model: 0.120 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 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 : 0.013 0.388 12843 Z= 1.103 Angle : 1.094 20.866 18610 Z= 0.924 Chirality : 0.065 0.782 2127 Planarity : 0.006 0.068 1347 Dihedral : 27.916 175.925 5523 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.16 % Allowed : 0.64 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 2.89 (0.30), residues: 751 helix: 2.82 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.54 (0.38), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG B 19 TYR 0.018 0.002 TYR B 88 PHE 0.012 0.001 PHE D 67 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.01276 / 1.10 (12843) covalent geometry : angle 1.09442 / 0.92 (18610) hydrogen bonds : bond 0.10856 / 7.25 ( 757) hydrogen bonds : angle 3.37182 / 2.51 ( 1911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.7865 (mt) cc_final: 0.7564 (mt) REVERT: C 41 GLU cc_start: 0.7525 (tt0) cc_final: 0.7219 (tt0) REVERT: C 99 ARG cc_start: 0.8802 (mmm-85) cc_final: 0.8033 (mmm160) REVERT: D 39 TYR cc_start: 0.8208 (t80) cc_final: 0.7930 (t80) REVERT: D 48 ASP cc_start: 0.8250 (p0) cc_final: 0.8002 (p0) REVERT: D 73 GLU cc_start: 0.8095 (tp30) cc_final: 0.7815 (tp30) REVERT: D 82 LYS cc_start: 0.8727 (mmtp) cc_final: 0.8498 (mmtt) REVERT: D 102 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7925 (mt-10) REVERT: G 90 ASP cc_start: 0.8076 (t0) cc_final: 0.7660 (t0) REVERT: G 95 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8672 (ttmm) REVERT: H 36 ILE cc_start: 0.8634 (mt) cc_final: 0.8324 (tp) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1457 time to fit residues: 35.9514 Evaluate side-chains 127 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN B 93 GLN C 24 GLN E 76 GLN F 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.080145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057877 restraints weight = 48604.762| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.48 r_work: 0.3055 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12843 Z= 0.166 Angle : 0.654 9.733 18610 Z= 0.396 Chirality : 0.046 0.436 2127 Planarity : 0.005 0.039 1347 Dihedral : 31.004 168.382 4045 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.11 % Allowed : 9.08 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 2.94 (0.30), residues: 751 helix: 2.85 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.62 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 96 TYR 0.009 0.001 TYR H 80 PHE 0.007 0.001 PHE H 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.17 (12843) covalent geometry : angle 0.65390 / 0.40 (18610) hydrogen bonds : bond 0.06258 / 4.16 ( 757) hydrogen bonds : angle 3.02016 / 2.17 ( 1911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8422 (pm20) cc_final: 0.7873 (pm20) REVERT: A 120 MET cc_start: 0.8582 (mmm) cc_final: 0.8382 (mmm) REVERT: A 125 GLN cc_start: 0.9195 (mt0) cc_final: 0.8952 (mt0) REVERT: C 56 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8640 (tt0) REVERT: C 90 ASP cc_start: 0.9197 (t0) cc_final: 0.8955 (t0) REVERT: D 48 ASP cc_start: 0.8432 (p0) cc_final: 0.8176 (p0) REVERT: D 80 TYR cc_start: 0.7791 (m-10) cc_final: 0.7581 (m-10) REVERT: E 120 MET cc_start: 0.7782 (mtt) cc_final: 0.7321 (mtt) REVERT: G 90 ASP cc_start: 0.8671 (t0) cc_final: 0.8455 (t0) REVERT: H 76 ARG cc_start: 0.8783 (ttm-80) cc_final: 0.8528 (mtt-85) outliers start: 7 outliers final: 4 residues processed: 142 average time/residue: 0.1150 time to fit residues: 22.7184 Evaluate side-chains 128 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 86 optimal weight: 40.0000 chunk 83 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 76 GLN C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.070663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.048561 restraints weight = 48406.518| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.48 r_work: 0.2790 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 12843 Z= 0.312 Angle : 0.823 10.162 18610 Z= 0.466 Chirality : 0.054 0.393 2127 Planarity : 0.007 0.047 1347 Dihedral : 31.864 162.723 4045 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.07 % Allowed : 10.51 % Favored : 87.42 % 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: 1.93 (0.29), residues: 751 helix: 2.07 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.92 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 89 TYR 0.018 0.003 TYR D 34 PHE 0.026 0.003 PHE C 25 HIS 0.007 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.31 (12843) covalent geometry : angle 0.82267 / 0.47 (18610) hydrogen bonds : bond 0.09073 / 6.18 ( 757) hydrogen bonds : angle 3.40156 / 2.41 ( 1911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8745 (pm20) cc_final: 0.8257 (pm20) REVERT: A 125 GLN cc_start: 0.9307 (mt0) cc_final: 0.9083 (mt0) REVERT: C 56 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8744 (tm-30) REVERT: D 48 ASP cc_start: 0.8682 (p0) cc_final: 0.8333 (p0) REVERT: D 65 ASP cc_start: 0.9254 (t0) cc_final: 0.8917 (t0) REVERT: D 80 TYR cc_start: 0.8068 (m-10) cc_final: 0.7792 (m-10) REVERT: G 90 ASP cc_start: 0.8822 (t0) cc_final: 0.8566 (t0) REVERT: H 76 ARG cc_start: 0.8852 (ttm-80) cc_final: 0.8579 (mtt-85) outliers start: 13 outliers final: 6 residues processed: 127 average time/residue: 0.1252 time to fit residues: 21.8564 Evaluate side-chains 116 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.072261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.050143 restraints weight = 47753.048| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.38 r_work: 0.2837 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12843 Z= 0.146 Angle : 0.609 7.199 18610 Z= 0.361 Chirality : 0.043 0.268 2127 Planarity : 0.004 0.036 1347 Dihedral : 31.525 166.611 4045 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.96 % Allowed : 13.06 % Favored : 85.99 % 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: 2.81 (0.30), residues: 751 helix: 2.79 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.84 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 29 TYR 0.017 0.001 TYR D 34 PHE 0.013 0.001 PHE C 25 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (12843) covalent geometry : angle 0.60937 / 0.36 (18610) hydrogen bonds : bond 0.04921 / 3.30 ( 757) hydrogen bonds : angle 2.87051 / 2.03 ( 1911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8661 (pm20) cc_final: 0.8268 (pm20) REVERT: A 125 GLN cc_start: 0.9238 (mt0) cc_final: 0.8977 (mt0) REVERT: C 56 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8729 (tt0) REVERT: D 48 ASP cc_start: 0.8654 (p0) cc_final: 0.8301 (p0) REVERT: D 65 ASP cc_start: 0.9235 (t0) cc_final: 0.8975 (t0) REVERT: D 80 TYR cc_start: 0.8063 (m-10) cc_final: 0.7746 (m-10) REVERT: E 73 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7375 (mt-10) REVERT: H 76 ARG cc_start: 0.8900 (ttm-80) cc_final: 0.8638 (mtt-85) outliers start: 6 outliers final: 5 residues processed: 121 average time/residue: 0.1208 time to fit residues: 20.2463 Evaluate side-chains 117 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 99 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.072078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.050170 restraints weight = 48250.154| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.34 r_work: 0.2843 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12843 Z= 0.150 Angle : 0.596 8.238 18610 Z= 0.354 Chirality : 0.042 0.257 2127 Planarity : 0.004 0.040 1347 Dihedral : 31.316 167.121 4045 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.91 % Allowed : 12.10 % Favored : 85.99 % 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: 3.07 (0.31), residues: 751 helix: 3.01 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.84 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 72 TYR 0.011 0.001 TYR D 34 PHE 0.010 0.001 PHE C 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (12843) covalent geometry : angle 0.59630 / 0.35 (18610) hydrogen bonds : bond 0.04846 / 3.27 ( 757) hydrogen bonds : angle 2.74982 / 1.94 ( 1911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: A 125 GLN cc_start: 0.9260 (mt0) cc_final: 0.9012 (mt0) REVERT: C 56 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8742 (tt0) REVERT: D 48 ASP cc_start: 0.8645 (p0) cc_final: 0.8326 (p0) REVERT: D 65 ASP cc_start: 0.9228 (t0) cc_final: 0.8957 (t0) REVERT: D 80 TYR cc_start: 0.7974 (m-10) cc_final: 0.7636 (m-10) outliers start: 12 outliers final: 8 residues processed: 122 average time/residue: 0.1176 time to fit residues: 19.8020 Evaluate side-chains 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.071513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.049673 restraints weight = 48246.086| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.40 r_work: 0.2827 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12843 Z= 0.154 Angle : 0.596 9.256 18610 Z= 0.352 Chirality : 0.041 0.263 2127 Planarity : 0.004 0.034 1347 Dihedral : 31.289 166.957 4045 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.91 % Allowed : 12.26 % Favored : 85.83 % 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: 3.15 (0.31), residues: 751 helix: 3.08 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.85 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.012 0.001 TYR D 34 PHE 0.011 0.001 PHE C 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (12843) covalent geometry : angle 0.59598 / 0.35 (18610) hydrogen bonds : bond 0.04507 / 3.03 ( 757) hydrogen bonds : angle 2.73863 / 1.93 ( 1911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: A 125 GLN cc_start: 0.9260 (mt0) cc_final: 0.9009 (mt0) REVERT: B 78 ARG cc_start: 0.8930 (mtm-85) cc_final: 0.8512 (mtm-85) REVERT: C 56 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8562 (tm-30) REVERT: D 48 ASP cc_start: 0.8664 (p0) cc_final: 0.8357 (p0) REVERT: D 65 ASP cc_start: 0.9250 (t0) cc_final: 0.8973 (t0) REVERT: D 80 TYR cc_start: 0.7963 (m-10) cc_final: 0.7649 (m-10) REVERT: E 59 GLU cc_start: 0.8892 (pm20) cc_final: 0.8599 (pm20) REVERT: H 31 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8392 (mptt) outliers start: 12 outliers final: 10 residues processed: 125 average time/residue: 0.1205 time to fit residues: 20.7882 Evaluate side-chains 128 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 chunk 43 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.065100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.044225 restraints weight = 48257.612| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.41 r_work: 0.2673 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 12843 Z= 0.393 Angle : 0.921 10.572 18610 Z= 0.491 Chirality : 0.056 0.296 2127 Planarity : 0.008 0.150 1347 Dihedral : 31.909 158.683 4045 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.39 % Allowed : 13.38 % Favored : 84.24 % 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: 1.73 (0.29), residues: 751 helix: 2.03 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -1.34 (0.37), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 30 TYR 0.021 0.003 TYR G 57 PHE 0.031 0.003 PHE C 25 HIS 0.009 0.003 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00829 / 0.39 (12843) covalent geometry : angle 0.92148 / 0.49 (18610) hydrogen bonds : bond 0.10156 / 6.81 ( 757) hydrogen bonds : angle 3.59727 / 2.55 ( 1911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8988 (tm-30) REVERT: D 48 ASP cc_start: 0.8870 (p0) cc_final: 0.8564 (p0) REVERT: D 80 TYR cc_start: 0.8255 (m-10) cc_final: 0.7831 (m-10) outliers start: 15 outliers final: 11 residues processed: 118 average time/residue: 0.1227 time to fit residues: 20.4306 Evaluate side-chains 115 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.068037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.046694 restraints weight = 48259.878| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.33 r_work: 0.2759 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12843 Z= 0.151 Angle : 0.636 8.877 18610 Z= 0.371 Chirality : 0.043 0.257 2127 Planarity : 0.004 0.032 1347 Dihedral : 31.527 166.012 4045 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.27 % Allowed : 14.49 % Favored : 84.24 % 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: 2.70 (0.30), residues: 751 helix: 2.77 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.05 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 30 TYR 0.015 0.002 TYR D 34 PHE 0.011 0.001 PHE B 61 HIS 0.002 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (12843) covalent geometry : angle 0.63613 / 0.37 (18610) hydrogen bonds : bond 0.04673 / 3.15 ( 757) hydrogen bonds : angle 2.90992 / 2.06 ( 1911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8792 (pm20) cc_final: 0.8356 (pm20) REVERT: B 88 TYR cc_start: 0.9275 (m-10) cc_final: 0.8742 (m-10) REVERT: C 56 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8758 (tm-30) REVERT: D 48 ASP cc_start: 0.8740 (p0) cc_final: 0.8458 (p0) REVERT: D 80 TYR cc_start: 0.8147 (m-10) cc_final: 0.7860 (m-10) REVERT: H 31 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8432 (mptt) outliers start: 8 outliers final: 6 residues processed: 120 average time/residue: 0.1173 time to fit residues: 19.9833 Evaluate side-chains 115 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 59 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.068291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046939 restraints weight = 48192.397| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.36 r_work: 0.2770 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12843 Z= 0.140 Angle : 0.618 11.256 18610 Z= 0.362 Chirality : 0.041 0.252 2127 Planarity : 0.004 0.039 1347 Dihedral : 31.336 166.636 4045 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.96 % Allowed : 14.49 % Favored : 84.55 % 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: 3.01 (0.31), residues: 751 helix: 3.01 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.97 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.012 0.001 TYR D 34 PHE 0.011 0.001 PHE E 67 HIS 0.002 0.000 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (12843) covalent geometry : angle 0.61789 / 0.36 (18610) hydrogen bonds : bond 0.04382 / 2.96 ( 757) hydrogen bonds : angle 2.77713 / 1.97 ( 1911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8751 (pm20) cc_final: 0.8245 (pm20) REVERT: C 56 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8758 (tm-30) REVERT: D 48 ASP cc_start: 0.8714 (p0) cc_final: 0.8436 (p0) REVERT: D 80 TYR cc_start: 0.8163 (m-10) cc_final: 0.7831 (m-10) REVERT: H 31 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8450 (mptt) outliers start: 6 outliers final: 5 residues processed: 119 average time/residue: 0.1068 time to fit residues: 18.4433 Evaluate side-chains 119 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 0.0170 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.068024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046805 restraints weight = 48156.272| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.32 r_work: 0.2767 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12843 Z= 0.154 Angle : 0.607 11.554 18610 Z= 0.356 Chirality : 0.041 0.259 2127 Planarity : 0.004 0.037 1347 Dihedral : 31.252 166.394 4045 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.11 % Allowed : 14.65 % Favored : 84.24 % 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: 3.05 (0.31), residues: 751 helix: 3.02 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.91 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.011 0.001 TYR C 57 PHE 0.010 0.001 PHE E 67 HIS 0.002 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (12843) covalent geometry : angle 0.60704 / 0.36 (18610) hydrogen bonds : bond 0.04313 / 2.92 ( 757) hydrogen bonds : angle 2.79012 / 1.98 ( 1911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8716 (pm20) cc_final: 0.8247 (pm20) REVERT: B 74 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8264 (tm-30) REVERT: B 88 TYR cc_start: 0.9237 (m-10) cc_final: 0.8630 (m-10) REVERT: C 56 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8730 (tm-30) REVERT: D 48 ASP cc_start: 0.8755 (p0) cc_final: 0.8482 (p0) REVERT: D 80 TYR cc_start: 0.8093 (m-10) cc_final: 0.7887 (m-10) REVERT: H 31 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8463 (mptt) outliers start: 7 outliers final: 6 residues processed: 117 average time/residue: 0.0839 time to fit residues: 14.2186 Evaluate side-chains 121 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 110 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.068048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.046749 restraints weight = 47783.669| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.37 r_work: 0.2760 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 12843 Z= 0.179 Angle : 0.838 59.200 18610 Z= 0.504 Chirality : 0.042 0.555 2127 Planarity : 0.004 0.037 1347 Dihedral : 31.255 166.422 4045 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.80 % Allowed : 14.97 % Favored : 84.24 % Cbeta Deviations : 0.14 % 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: 3.05 (0.31), residues: 751 helix: 3.02 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.90 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.032 0.002 TYR G 57 PHE 0.010 0.001 PHE E 67 HIS 0.002 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.18 (12843) covalent geometry : angle 0.83784 / 0.50 (18610) hydrogen bonds : bond 0.04294 / 2.90 ( 757) hydrogen bonds : angle 2.79016 / 1.98 ( 1911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2624.64 seconds wall clock time: 45 minutes 28.32 seconds (2728.32 seconds total)