Starting phenix.real_space_refine on Fri Jul 3 04:45:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cau_45404/07_2026/9cau_45404_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cau_45404/07_2026/9cau_45404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cau_45404/07_2026/9cau_45404_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cau_45404/07_2026/9cau_45404_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cau_45404/07_2026/9cau_45404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cau_45404/07_2026/9cau_45404.map" } resolution = 4.18 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= 0.001 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 4 5.16 5 C 6589 2.51 5 N 2240 2.21 5 O 2824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s 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: 11949 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2976 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU B 23 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 23 " occ=0.00 residue: pdb=" N ARG B 24 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 24 " occ=0.00 Time building chain proxies: 2.45, per 1000 atoms: 0.21 Number of scatterers: 11949 At special positions: 0 Unit cell: (117.103, 99.0869, 144.126, 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 4 16.00 P 292 15.00 O 2824 8.00 N 2240 7.00 C 6589 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: 0.84 Conformation dependent library (CDL) restraints added in 144.8 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 7 sheets defined 69.2% alpha, 1.9% beta 143 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.502A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.877A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.521A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 43 removed outlier: 3.612A pdb=" N ILE B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.359A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 4.275A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.200A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.625A pdb=" N ASN C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 40 through 52 Processing helix chain 'D' and resid 58 through 87 removed outlier: 3.638A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 105 removed outlier: 4.099A pdb=" N ILE D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 127 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.720A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 31 through 43 Processing helix chain 'F' and resid 50 through 77 removed outlier: 4.467A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN F 65 " --> pdb=" O VAL F 61 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 66 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 4.067A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.212A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 58 through 88 removed outlier: 3.503A pdb=" N ASN H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.660A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 126 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.977A pdb=" N ARG A 83 " --> pdb=" O VAL B 82 " (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 'C' and resid 43 through 44 removed outlier: 6.577A pdb=" N ARG C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.135A pdb=" N ARG G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 78 through 79 373 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2065 1.33 - 1.45: 4512 1.45 - 1.58: 5588 1.58 - 1.70: 582 1.70 - 1.82: 8 Bond restraints: 12755 Sorted by residual: bond pdb=" C1' DC I 37 " pdb=" N1 DC I 37 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.95e+01 bond pdb=" C1' DT I -61 " pdb=" N1 DT I -61 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.93e+01 bond pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.30e-02 5.92e+03 1.58e+01 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.47e+01 bond pdb=" C1' DC J 49 " pdb=" N1 DC J 49 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.28e+01 ... (remaining 12750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 18105 3.06 - 6.12: 319 6.12 - 9.17: 38 9.17 - 12.23: 10 12.23 - 15.29: 5 Bond angle restraints: 18477 Sorted by residual: angle pdb=" N GLY H 107 " pdb=" CA GLY H 107 " pdb=" C GLY H 107 " ideal model delta sigma weight residual 112.73 119.89 -7.16 1.20e+00 6.94e-01 3.56e+01 angle pdb=" CB GLN A 93 " pdb=" CG GLN A 93 " pdb=" CD GLN A 93 " ideal model delta sigma weight residual 112.60 102.95 9.65 1.70e+00 3.46e-01 3.22e+01 angle pdb=" C GLY D 107 " pdb=" N GLU D 108 " pdb=" CA GLU D 108 " ideal model delta sigma weight residual 121.54 132.17 -10.63 1.91e+00 2.74e-01 3.10e+01 angle pdb=" N GLU B 64 " pdb=" CA GLU B 64 " pdb=" CB GLU B 64 " ideal model delta sigma weight residual 110.30 118.72 -8.42 1.54e+00 4.22e-01 2.99e+01 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.89e+01 ... (remaining 18472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 5450 35.72 - 71.44: 1432 71.44 - 107.16: 28 107.16 - 142.88: 0 142.88 - 178.60: 3 Dihedral angle restraints: 6913 sinusoidal: 4727 harmonic: 2186 Sorted by residual: dihedral pdb=" CA ILE F 51 " pdb=" C ILE F 51 " pdb=" N TYR F 52 " pdb=" CA TYR F 52 " ideal model delta harmonic sigma weight residual -180.00 -151.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ASN B 65 " pdb=" C ASN B 65 " pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LYS B 80 " pdb=" C LYS B 80 " pdb=" N THR B 81 " pdb=" CA THR B 81 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 6910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1461 0.053 - 0.106: 499 0.106 - 0.159: 115 0.159 - 0.212: 25 0.212 - 0.265: 5 Chirality restraints: 2105 Sorted by residual: chirality pdb=" CB VAL A 96 " pdb=" CA VAL A 96 " pdb=" CG1 VAL A 96 " pdb=" CG2 VAL A 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU H 105 " pdb=" CB LEU H 105 " pdb=" CD1 LEU H 105 " pdb=" CD2 LEU H 105 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB THR H 118 " pdb=" CA THR H 118 " pdb=" OG1 THR H 118 " pdb=" CG2 THR H 118 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2102 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 67 " -0.010 2.00e-02 2.50e+03 2.78e-02 1.35e+01 pdb=" CG PHE A 67 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 67 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 67 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE A 67 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 67 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 89 " 0.024 2.00e-02 2.50e+03 2.34e-02 1.10e+01 pdb=" CG TYR B 89 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR B 89 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 89 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 89 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 89 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 89 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 89 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 73 " -0.013 2.00e-02 2.50e+03 2.42e-02 1.03e+01 pdb=" CG PHE H 73 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE H 73 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE H 73 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE H 73 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 73 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE H 73 " 0.001 2.00e-02 2.50e+03 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 3493 2.86 - 3.37: 10831 3.37 - 3.88: 24645 3.88 - 4.39: 27217 4.39 - 4.90: 37204 Nonbonded interactions: 103390 Sorted by model distance: nonbonded pdb=" NH1 ARG C 33 " pdb=" OP1 DA J -44 " model vdw 2.345 3.120 nonbonded pdb=" O HIS B 76 " pdb=" NH1 ARG D 95 " model vdw 2.356 3.120 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 26 " model vdw 2.360 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE2 GLU E 133 " model vdw 2.364 3.040 nonbonded pdb=" OH TYR D 43 " pdb=" OP1 DG I 48 " model vdw 2.371 3.040 ... (remaining 103385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 25 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 103)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 120)) selection = (chain 'G' and resid 16 through 120) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.650 Find NCS groups from input model: 0.070 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 12755 Z= 0.566 Angle : 1.128 15.291 18477 Z= 0.833 Chirality : 0.057 0.265 2105 Planarity : 0.008 0.071 1327 Dihedral : 29.098 178.598 5501 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -2.58 (0.26), residues: 738 helix: -1.61 (0.19), residues: 508 sheet: None (None), residues: 0 loop : -1.51 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 89 TYR 0.058 0.004 TYR B 89 PHE 0.058 0.004 PHE A 67 HIS 0.013 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.57 (12755) covalent geometry : angle 1.12795 / 0.83 (18477) hydrogen bonds : bond 0.10902 / 7.56 ( 741) hydrogen bonds : angle 5.14104 / 3.56 ( 1855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.6691 (mmm160) cc_final: 0.5255 (ttp80) REVERT: A 50 GLU cc_start: 0.8394 (pp20) cc_final: 0.8137 (pp20) REVERT: A 56 LYS cc_start: 0.8486 (tptp) cc_final: 0.8275 (tmtt) REVERT: A 58 THR cc_start: 0.7629 (m) cc_final: 0.7252 (t) REVERT: A 94 GLU cc_start: 0.8386 (tt0) cc_final: 0.7675 (tt0) REVERT: A 105 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 131 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8256 (mmm-85) REVERT: B 51 ILE cc_start: 0.8407 (mm) cc_final: 0.7764 (mt) REVERT: B 80 LYS cc_start: 0.8726 (pttm) cc_final: 0.7951 (ttmm) REVERT: B 85 MET cc_start: 0.8177 (mmm) cc_final: 0.7311 (tpp) REVERT: C 37 ARG cc_start: 0.8238 (ptp90) cc_final: 0.8035 (ptp90) REVERT: C 42 GLN cc_start: 0.7677 (pp30) cc_final: 0.7307 (pp30) REVERT: C 43 ARG cc_start: 0.7745 (ttp-110) cc_final: 0.7505 (mtp85) REVERT: C 46 SER cc_start: 0.8773 (p) cc_final: 0.8517 (m) REVERT: C 111 ASN cc_start: 0.8685 (m110) cc_final: 0.8418 (m110) REVERT: D 71 ASP cc_start: 0.9022 (t70) cc_final: 0.8667 (t0) REVERT: D 124 TYR cc_start: 0.8874 (t80) cc_final: 0.8621 (t80) REVERT: E 59 GLU cc_start: 0.8561 (tp30) cc_final: 0.7883 (pp20) REVERT: E 60 LEU cc_start: 0.8836 (mt) cc_final: 0.8404 (mm) REVERT: E 61 LEU cc_start: 0.8695 (mt) cc_final: 0.8264 (mt) REVERT: E 74 ILE cc_start: 0.9038 (tt) cc_final: 0.8431 (mm) REVERT: E 78 PHE cc_start: 0.7821 (m-10) cc_final: 0.7046 (m-10) REVERT: E 121 LYS cc_start: 0.8932 (ptmm) cc_final: 0.8672 (ptmt) REVERT: F 27 ILE cc_start: 0.7599 (mm) cc_final: 0.7090 (mp) REVERT: F 50 LEU cc_start: 0.9035 (pt) cc_final: 0.8570 (tp) REVERT: F 63 LEU cc_start: 0.9215 (pp) cc_final: 0.8880 (mp) REVERT: F 68 ARG cc_start: 0.8712 (mtm110) cc_final: 0.8489 (mtm-85) REVERT: G 21 LYS cc_start: 0.8733 (tmtt) cc_final: 0.8197 (tptt) REVERT: G 57 GLU cc_start: 0.8197 (tt0) cc_final: 0.7858 (tt0) REVERT: G 69 ASN cc_start: 0.8717 (m-40) cc_final: 0.8441 (m-40) REVERT: G 86 LEU cc_start: 0.9019 (mt) cc_final: 0.8656 (mt) REVERT: G 93 GLU cc_start: 0.8110 (pt0) cc_final: 0.7605 (pt0) REVERT: G 95 ASN cc_start: 0.8660 (m-40) cc_final: 0.8189 (m110) REVERT: G 98 LEU cc_start: 0.9250 (mm) cc_final: 0.8998 (mm) REVERT: G 103 ILE cc_start: 0.9117 (mp) cc_final: 0.8874 (pt) REVERT: G 115 ASN cc_start: 0.7625 (t0) cc_final: 0.7372 (t0) REVERT: H 55 THR cc_start: 0.8821 (m) cc_final: 0.8424 (m) REVERT: H 71 ASP cc_start: 0.8998 (t70) cc_final: 0.8517 (t0) REVERT: H 79 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8917 (tm-30) REVERT: H 112 HIS cc_start: 0.8691 (m170) cc_final: 0.8135 (m90) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.1461 time to fit residues: 61.5689 Evaluate side-chains 215 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0040 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 HIS ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 68 GLN E 108 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.077693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.056256 restraints weight = 66556.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.057311 restraints weight = 36315.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058013 restraints weight = 25526.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058464 restraints weight = 20907.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.058667 restraints weight = 18752.881| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12755 Z= 0.163 Angle : 0.714 10.141 18477 Z= 0.417 Chirality : 0.048 0.246 2105 Planarity : 0.006 0.060 1327 Dihedral : 32.204 178.768 4019 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.48 % Allowed : 4.46 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.01 (0.29), residues: 738 helix: -0.28 (0.21), residues: 517 sheet: None (None), residues: 0 loop : -1.31 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 79 TYR 0.035 0.003 TYR H 86 PHE 0.023 0.002 PHE E 104 HIS 0.009 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (12755) covalent geometry : angle 0.71418 / 0.42 (18477) hydrogen bonds : bond 0.04771 / 3.15 ( 741) hydrogen bonds : angle 3.65935 / 2.58 ( 1855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 255 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.6391 (mmm160) cc_final: 0.4507 (ttp80) REVERT: A 45 THR cc_start: 0.8366 (t) cc_final: 0.8040 (t) REVERT: A 59 GLU cc_start: 0.7239 (mp0) cc_final: 0.6954 (mp0) REVERT: A 73 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7250 (mt-10) REVERT: A 105 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 80 LYS cc_start: 0.8551 (pttm) cc_final: 0.7795 (ttmm) REVERT: B 85 MET cc_start: 0.7624 (mmm) cc_final: 0.7242 (tpt) REVERT: C 42 GLN cc_start: 0.7718 (pp30) cc_final: 0.7364 (pp30) REVERT: C 69 ASN cc_start: 0.8774 (m110) cc_final: 0.8562 (m110) REVERT: D 51 THR cc_start: 0.8616 (t) cc_final: 0.8365 (t) REVERT: D 74 GLU cc_start: 0.8677 (pt0) cc_final: 0.8448 (pt0) REVERT: D 119 ARG cc_start: 0.8853 (tmm160) cc_final: 0.8605 (ttp80) REVERT: E 77 ASP cc_start: 0.8493 (p0) cc_final: 0.8283 (p0) REVERT: E 95 SER cc_start: 0.9607 (t) cc_final: 0.9204 (p) REVERT: E 105 GLU cc_start: 0.8782 (tt0) cc_final: 0.8276 (tp30) REVERT: E 121 LYS cc_start: 0.9064 (ptmm) cc_final: 0.8843 (ptmt) REVERT: F 45 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8767 (mtpp) REVERT: F 50 LEU cc_start: 0.8737 (pt) cc_final: 0.8502 (tp) REVERT: G 21 LYS cc_start: 0.8900 (tmtt) cc_final: 0.8549 (tptt) REVERT: G 74 ASN cc_start: 0.8893 (t0) cc_final: 0.8631 (t0) REVERT: G 93 GLU cc_start: 0.7555 (pt0) cc_final: 0.6884 (pt0) REVERT: H 48 LEU cc_start: 0.9343 (pt) cc_final: 0.9058 (pt) REVERT: H 82 LYS cc_start: 0.9042 (ttmm) cc_final: 0.8552 (tptp) outliers start: 3 outliers final: 0 residues processed: 256 average time/residue: 0.1297 time to fit residues: 43.4999 Evaluate side-chains 195 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 68 GLN G 42 GLN H 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.076568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.054169 restraints weight = 67790.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055189 restraints weight = 37799.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.055898 restraints weight = 26910.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056318 restraints weight = 22314.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056515 restraints weight = 20188.051| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12755 Z= 0.165 Angle : 0.661 9.344 18477 Z= 0.391 Chirality : 0.045 0.251 2105 Planarity : 0.005 0.058 1327 Dihedral : 32.021 178.404 4019 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.64 % Allowed : 4.30 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.08 (0.30), residues: 738 helix: 0.54 (0.22), residues: 511 sheet: None (None), residues: 0 loop : -1.28 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 69 TYR 0.048 0.003 TYR H 86 PHE 0.014 0.002 PHE H 73 HIS 0.007 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (12755) covalent geometry : angle 0.66070 / 0.39 (18477) hydrogen bonds : bond 0.04656 / 3.08 ( 741) hydrogen bonds : angle 3.32611 / 2.35 ( 1855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 244 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.6301 (mmm160) cc_final: 0.4501 (ttp80) REVERT: A 59 GLU cc_start: 0.7525 (mp0) cc_final: 0.7313 (mp0) REVERT: A 94 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7640 (tt0) REVERT: A 105 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 89 TYR cc_start: 0.7998 (m-80) cc_final: 0.7274 (m-80) REVERT: C 18 ARG cc_start: 0.8142 (ttt180) cc_final: 0.7672 (ttt180) REVERT: C 42 GLN cc_start: 0.7542 (pp30) cc_final: 0.6964 (pp30) REVERT: C 69 ASN cc_start: 0.8827 (m110) cc_final: 0.8617 (m110) REVERT: D 38 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7274 (pt0) REVERT: D 86 TYR cc_start: 0.8592 (m-80) cc_final: 0.8234 (m-80) REVERT: D 109 LEU cc_start: 0.9031 (mp) cc_final: 0.8093 (mp) REVERT: D 119 ARG cc_start: 0.8860 (tmm160) cc_final: 0.8600 (ttp80) REVERT: E 95 SER cc_start: 0.9653 (t) cc_final: 0.9328 (p) REVERT: E 105 GLU cc_start: 0.8745 (tt0) cc_final: 0.8282 (tp30) REVERT: F 45 LYS cc_start: 0.9119 (mtpt) cc_final: 0.8827 (mtpp) REVERT: F 50 LEU cc_start: 0.8700 (pt) cc_final: 0.8467 (tp) REVERT: F 68 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8000 (mtm-85) REVERT: F 75 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7921 (tm-30) REVERT: F 78 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8783 (mppt) REVERT: G 21 LYS cc_start: 0.8958 (tmtt) cc_final: 0.8583 (tptt) REVERT: G 74 ASN cc_start: 0.8931 (t0) cc_final: 0.8620 (t0) REVERT: G 91 ASP cc_start: 0.9028 (t0) cc_final: 0.8804 (t0) REVERT: G 93 GLU cc_start: 0.7524 (pt0) cc_final: 0.6706 (pt0) outliers start: 4 outliers final: 0 residues processed: 246 average time/residue: 0.1236 time to fit residues: 40.4223 Evaluate side-chains 188 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 108 ASN F 94 GLN G 42 GLN H 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.076492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.054275 restraints weight = 66837.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.055293 restraints weight = 36769.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.055979 restraints weight = 26173.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056339 restraints weight = 21679.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056600 restraints weight = 19747.099| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12755 Z= 0.154 Angle : 0.648 9.615 18477 Z= 0.381 Chirality : 0.044 0.247 2105 Planarity : 0.005 0.055 1327 Dihedral : 31.950 179.971 4019 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.16 % Allowed : 5.10 % Favored : 94.75 % 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: 0.31 (0.30), residues: 738 helix: 0.85 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -1.20 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 69 TYR 0.040 0.002 TYR B 52 PHE 0.019 0.002 PHE B 101 HIS 0.007 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (12755) covalent geometry : angle 0.64828 / 0.38 (18477) hydrogen bonds : bond 0.04291 / 2.83 ( 741) hydrogen bonds : angle 3.23390 / 2.28 ( 1855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.6254 (mmm160) cc_final: 0.4475 (ttp80) REVERT: A 59 GLU cc_start: 0.7494 (mp0) cc_final: 0.7246 (mp0) REVERT: A 105 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 64 GLU cc_start: 0.8742 (pm20) cc_final: 0.8469 (mp0) REVERT: B 89 TYR cc_start: 0.8162 (m-80) cc_final: 0.7954 (m-80) REVERT: C 42 GLN cc_start: 0.7678 (pp30) cc_final: 0.7056 (pp30) REVERT: D 38 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7250 (pt0) REVERT: D 109 LEU cc_start: 0.9019 (mp) cc_final: 0.8728 (mt) REVERT: D 119 ARG cc_start: 0.8898 (tmm160) cc_final: 0.8622 (ttp80) REVERT: E 77 ASP cc_start: 0.8743 (p0) cc_final: 0.8323 (p0) REVERT: E 95 SER cc_start: 0.9638 (t) cc_final: 0.9280 (p) REVERT: E 105 GLU cc_start: 0.8756 (tt0) cc_final: 0.8306 (tp30) REVERT: F 45 LYS cc_start: 0.9077 (mtpt) cc_final: 0.8757 (mttp) REVERT: F 50 LEU cc_start: 0.8689 (pt) cc_final: 0.7874 (tt) REVERT: F 75 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7923 (tm-30) REVERT: G 21 LYS cc_start: 0.8962 (tmtt) cc_final: 0.8528 (tptt) REVERT: G 74 ASN cc_start: 0.8936 (t0) cc_final: 0.8531 (t0) REVERT: G 91 ASP cc_start: 0.8952 (t0) cc_final: 0.8739 (t0) REVERT: G 93 GLU cc_start: 0.7469 (pt0) cc_final: 0.6761 (pt0) REVERT: H 79 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8688 (tp30) REVERT: H 112 HIS cc_start: 0.8339 (m170) cc_final: 0.7973 (m90) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1126 time to fit residues: 35.9892 Evaluate side-chains 188 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.0040 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 75 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 68 GLN F 94 GLN G 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.076455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.054086 restraints weight = 66460.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055100 restraints weight = 36625.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.055773 restraints weight = 25995.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.056172 restraints weight = 21589.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.056281 restraints weight = 19598.699| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12755 Z= 0.147 Angle : 0.636 9.243 18477 Z= 0.373 Chirality : 0.044 0.247 2105 Planarity : 0.005 0.064 1327 Dihedral : 31.880 179.810 4019 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.16 % Allowed : 2.55 % Favored : 97.29 % 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: 0.45 (0.30), residues: 738 helix: 0.92 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.09 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 69 TYR 0.043 0.002 TYR H 86 PHE 0.010 0.001 PHE B 101 HIS 0.007 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.15 (12755) covalent geometry : angle 0.63628 / 0.37 (18477) hydrogen bonds : bond 0.04139 / 2.72 ( 741) hydrogen bonds : angle 3.20747 / 2.28 ( 1855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7636 (mp0) cc_final: 0.7369 (mp0) REVERT: A 105 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 51 ILE cc_start: 0.8376 (mm) cc_final: 0.7828 (mt) REVERT: B 64 GLU cc_start: 0.8744 (pm20) cc_final: 0.8511 (pm20) REVERT: B 89 TYR cc_start: 0.8008 (m-80) cc_final: 0.6791 (m-80) REVERT: D 38 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7194 (pt0) REVERT: D 82 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8459 (mttm) REVERT: D 86 TYR cc_start: 0.8481 (m-80) cc_final: 0.7560 (m-80) REVERT: D 119 ARG cc_start: 0.8931 (tmm160) cc_final: 0.8645 (ttp80) REVERT: E 95 SER cc_start: 0.9651 (t) cc_final: 0.9277 (p) REVERT: E 105 GLU cc_start: 0.8753 (tt0) cc_final: 0.8310 (tp30) REVERT: E 133 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7165 (mt-10) REVERT: F 40 ARG cc_start: 0.8928 (mmt90) cc_final: 0.8645 (tpp80) REVERT: F 50 LEU cc_start: 0.8634 (pt) cc_final: 0.7998 (tt) REVERT: G 21 LYS cc_start: 0.8980 (tttt) cc_final: 0.8555 (tptt) REVERT: G 74 ASN cc_start: 0.8917 (t0) cc_final: 0.8570 (t0) REVERT: G 91 ASP cc_start: 0.8923 (t0) cc_final: 0.8719 (t0) REVERT: G 93 GLU cc_start: 0.7677 (pt0) cc_final: 0.6763 (pt0) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1172 time to fit residues: 35.5053 Evaluate side-chains 173 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.075947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053767 restraints weight = 65667.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.054762 restraints weight = 35668.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.055420 restraints weight = 25304.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.055811 restraints weight = 21056.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.056029 restraints weight = 19141.011| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12755 Z= 0.151 Angle : 0.649 11.681 18477 Z= 0.373 Chirality : 0.044 0.248 2105 Planarity : 0.005 0.058 1327 Dihedral : 31.836 179.941 4019 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.32 % Allowed : 3.82 % Favored : 95.86 % 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: 0.61 (0.31), residues: 738 helix: 1.06 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.13 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 68 TYR 0.027 0.002 TYR B 52 PHE 0.011 0.002 PHE B 101 HIS 0.007 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (12755) covalent geometry : angle 0.64907 / 0.37 (18477) hydrogen bonds : bond 0.04097 / 2.68 ( 741) hydrogen bonds : angle 3.13799 / 2.21 ( 1855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7681 (tm-30) REVERT: D 38 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7166 (pt0) REVERT: D 86 TYR cc_start: 0.8609 (m-80) cc_final: 0.7931 (m-80) REVERT: E 105 GLU cc_start: 0.8809 (tt0) cc_final: 0.8270 (tp30) REVERT: F 40 ARG cc_start: 0.8865 (mmt90) cc_final: 0.8524 (tpp80) REVERT: F 45 LYS cc_start: 0.9113 (mtpt) cc_final: 0.8862 (mttp) REVERT: F 50 LEU cc_start: 0.8634 (pt) cc_final: 0.7924 (tt) REVERT: F 68 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8185 (mtm110) REVERT: G 21 LYS cc_start: 0.9035 (tttt) cc_final: 0.8710 (tptt) REVERT: G 30 ARG cc_start: 0.8681 (ttm170) cc_final: 0.8477 (ttm170) REVERT: G 42 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: G 74 ASN cc_start: 0.8986 (t0) cc_final: 0.8618 (t0) REVERT: G 82 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8338 (tpp80) REVERT: G 93 GLU cc_start: 0.7642 (pt0) cc_final: 0.6753 (pt0) REVERT: H 89 LYS cc_start: 0.8523 (tppt) cc_final: 0.8293 (mmtt) REVERT: H 116 GLU cc_start: 0.7809 (tp30) cc_final: 0.7346 (tp30) outliers start: 2 outliers final: 0 residues processed: 217 average time/residue: 0.1222 time to fit residues: 35.0954 Evaluate side-chains 178 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 68 GLN H 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.075808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053690 restraints weight = 65179.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.054628 restraints weight = 35775.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.055263 restraints weight = 25475.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055446 restraints weight = 21270.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055789 restraints weight = 19822.402| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12755 Z= 0.149 Angle : 0.644 9.114 18477 Z= 0.372 Chirality : 0.044 0.251 2105 Planarity : 0.005 0.068 1327 Dihedral : 31.805 179.767 4019 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.31), residues: 738 helix: 1.13 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.10 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 69 TYR 0.057 0.003 TYR H 86 PHE 0.022 0.002 PHE C 26 HIS 0.008 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (12755) covalent geometry : angle 0.64442 / 0.37 (18477) hydrogen bonds : bond 0.04065 / 2.66 ( 741) hydrogen bonds : angle 3.13603 / 2.22 ( 1855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7679 (tm-30) REVERT: D 38 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7090 (pt0) REVERT: D 82 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8432 (mttp) REVERT: D 86 TYR cc_start: 0.8600 (m-80) cc_final: 0.7932 (m-80) REVERT: E 105 GLU cc_start: 0.8804 (tt0) cc_final: 0.8267 (tp30) REVERT: F 40 ARG cc_start: 0.8863 (mmt90) cc_final: 0.8489 (tpp80) REVERT: F 45 LYS cc_start: 0.9144 (mtpt) cc_final: 0.8883 (mttp) REVERT: F 50 LEU cc_start: 0.8656 (pt) cc_final: 0.7973 (tt) REVERT: F 89 TYR cc_start: 0.7488 (m-10) cc_final: 0.7191 (m-10) REVERT: G 21 LYS cc_start: 0.9073 (tttt) cc_final: 0.8723 (tptt) REVERT: G 74 ASN cc_start: 0.8911 (t0) cc_final: 0.8645 (t0) REVERT: G 82 ARG cc_start: 0.8581 (tpp80) cc_final: 0.8240 (tpp80) REVERT: G 93 GLU cc_start: 0.7581 (pt0) cc_final: 0.6942 (pt0) REVERT: H 50 GLN cc_start: 0.8832 (pt0) cc_final: 0.8560 (pp30) REVERT: H 86 TYR cc_start: 0.8277 (m-10) cc_final: 0.8011 (m-80) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1260 time to fit residues: 36.0919 Evaluate side-chains 168 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 30.0000 chunk 94 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 85 optimal weight: 40.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS D 50 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 76 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.075324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.053073 restraints weight = 65597.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054031 restraints weight = 35414.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.054675 restraints weight = 25132.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055056 restraints weight = 20979.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.055244 restraints weight = 19071.036| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12755 Z= 0.159 Angle : 0.650 8.058 18477 Z= 0.376 Chirality : 0.044 0.255 2105 Planarity : 0.005 0.057 1327 Dihedral : 31.819 179.669 4019 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.16 % Allowed : 1.91 % Favored : 97.93 % 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 (0.31), residues: 738 helix: 1.18 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.11 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 119 TYR 0.048 0.003 TYR H 86 PHE 0.015 0.002 PHE E 54 HIS 0.007 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (12755) covalent geometry : angle 0.65035 / 0.38 (18477) hydrogen bonds : bond 0.04199 / 2.76 ( 741) hydrogen bonds : angle 3.16558 / 2.24 ( 1855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7671 (tm-30) REVERT: D 38 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7086 (pt0) REVERT: D 86 TYR cc_start: 0.8652 (m-80) cc_final: 0.7965 (m-80) REVERT: D 119 ARG cc_start: 0.9092 (ttp80) cc_final: 0.8886 (ttp80) REVERT: E 105 GLU cc_start: 0.8848 (tt0) cc_final: 0.8308 (tp30) REVERT: F 40 ARG cc_start: 0.8947 (mmt90) cc_final: 0.8690 (tpp80) REVERT: F 50 LEU cc_start: 0.8677 (pt) cc_final: 0.7984 (tt) REVERT: G 21 LYS cc_start: 0.9132 (tttt) cc_final: 0.8731 (tptt) REVERT: G 74 ASN cc_start: 0.8942 (t0) cc_final: 0.8681 (t0) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1229 time to fit residues: 34.3959 Evaluate side-chains 161 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 10.9990 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 86 optimal weight: 30.0000 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN H 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.074598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052276 restraints weight = 65167.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053224 restraints weight = 35183.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053854 restraints weight = 25005.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.054232 restraints weight = 20909.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.054443 restraints weight = 19022.293| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12755 Z= 0.175 Angle : 0.693 10.418 18477 Z= 0.391 Chirality : 0.044 0.261 2105 Planarity : 0.005 0.061 1327 Dihedral : 31.859 179.263 4019 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 0.63 (0.31), residues: 738 helix: 1.09 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.15 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 69 TYR 0.074 0.003 TYR H 86 PHE 0.015 0.002 PHE C 26 HIS 0.009 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (12755) covalent geometry : angle 0.69344 / 0.39 (18477) hydrogen bonds : bond 0.04423 / 2.91 ( 741) hydrogen bonds : angle 3.20606 / 2.28 ( 1855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7705 (tm-30) REVERT: B 54 GLU cc_start: 0.8725 (pp20) cc_final: 0.8518 (pp20) REVERT: D 38 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7079 (pt0) REVERT: D 82 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8647 (mttp) REVERT: D 86 TYR cc_start: 0.8649 (m-80) cc_final: 0.8056 (m-80) REVERT: E 105 GLU cc_start: 0.8876 (tt0) cc_final: 0.8332 (tp30) REVERT: F 40 ARG cc_start: 0.8911 (mmt90) cc_final: 0.8691 (tpp80) REVERT: F 50 LEU cc_start: 0.8719 (pt) cc_final: 0.8032 (tt) REVERT: G 74 ASN cc_start: 0.8983 (t0) cc_final: 0.8727 (t0) REVERT: G 93 GLU cc_start: 0.7639 (pt0) cc_final: 0.7405 (pm20) REVERT: H 116 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7922 (mm-30) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1234 time to fit residues: 34.2503 Evaluate side-chains 167 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 85 optimal weight: 40.0000 chunk 97 optimal weight: 10.9990 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN C 39 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN G 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.074008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.051573 restraints weight = 65536.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.052499 restraints weight = 36376.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053086 restraints weight = 26236.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.053450 restraints weight = 22115.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053524 restraints weight = 20235.867| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12755 Z= 0.202 Angle : 0.703 9.712 18477 Z= 0.399 Chirality : 0.045 0.267 2105 Planarity : 0.005 0.059 1327 Dihedral : 31.938 178.918 4019 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.16 % Allowed : 0.80 % Favored : 99.04 % 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: 0.55 (0.30), residues: 738 helix: 1.04 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.22 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 69 TYR 0.037 0.003 TYR H 86 PHE 0.014 0.002 PHE E 104 HIS 0.009 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 (12755) covalent geometry : angle 0.70287 / 0.40 (18477) hydrogen bonds : bond 0.04833 / 3.22 ( 741) hydrogen bonds : angle 3.29908 / 2.36 ( 1855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7701 (tm-30) REVERT: D 38 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7078 (pt0) REVERT: D 82 LYS cc_start: 0.8824 (mtmm) cc_final: 0.8475 (mttp) REVERT: D 86 TYR cc_start: 0.8660 (m-80) cc_final: 0.8113 (m-80) REVERT: E 105 GLU cc_start: 0.8860 (tt0) cc_final: 0.8349 (tp30) REVERT: F 40 ARG cc_start: 0.8840 (mmt90) cc_final: 0.8634 (tpp80) REVERT: G 92 ASP cc_start: 0.9084 (p0) cc_final: 0.8846 (p0) REVERT: G 93 GLU cc_start: 0.7605 (pt0) cc_final: 0.7369 (pm20) REVERT: H 50 GLN cc_start: 0.8876 (pt0) cc_final: 0.8574 (pp30) REVERT: H 116 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7788 (mm-30) REVERT: H 119 ARG cc_start: 0.8693 (ptm-80) cc_final: 0.7993 (ptm-80) outliers start: 1 outliers final: 1 residues processed: 203 average time/residue: 0.1279 time to fit residues: 34.4427 Evaluate side-chains 165 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 63 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.075139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052948 restraints weight = 65024.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053906 restraints weight = 35551.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.054515 restraints weight = 25451.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.054890 restraints weight = 21339.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054966 restraints weight = 19482.560| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12755 Z= 0.152 Angle : 0.677 10.029 18477 Z= 0.385 Chirality : 0.044 0.260 2105 Planarity : 0.005 0.058 1327 Dihedral : 31.870 179.377 4019 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.31), residues: 738 helix: 1.10 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.16 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 69 TYR 0.030 0.003 TYR B 89 PHE 0.019 0.002 PHE A 67 HIS 0.007 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (12755) covalent geometry : angle 0.67687 / 0.38 (18477) hydrogen bonds : bond 0.04046 / 2.67 ( 741) hydrogen bonds : angle 3.22476 / 2.30 ( 1855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1964.49 seconds wall clock time: 34 minutes 33.73 seconds (2073.73 seconds total)