Starting phenix.real_space_refine on Wed Jul 30 08:29:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cau_45404/07_2025/9cau_45404_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cau_45404/07_2025/9cau_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cau_45404/07_2025/9cau_45404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cau_45404/07_2025/9cau_45404.map" model { file = "/net/cci-nas-00/data/ceres_data/9cau_45404/07_2025/9cau_45404_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cau_45404/07_2025/9cau_45404_neut.cif" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.33, per 1000 atoms: 0.70 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: 2.96 Conformation dependent library (CDL) restraints added in 974.4 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: 6.17 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: 4.24 Time building geometry restraints manager: 3.53 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=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.422 1.487 -0.065 3.00e-02 1.11e+03 4.66e+00 bond pdb=" CB GLN A 93 " pdb=" CG GLN A 93 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.53e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.38e+00 bond pdb=" CD GLU B 64 " pdb=" OE1 GLU B 64 " ideal model delta sigma weight residual 1.249 1.211 0.038 1.90e-02 2.77e+03 4.01e+00 bond pdb=" C3' DG J 52 " pdb=" O3' DG J 52 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.20e+00 ... (remaining 12750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 18152 3.06 - 6.12: 272 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: 1603 0.053 - 0.106: 368 0.106 - 0.159: 106 0.159 - 0.212: 23 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: 20.690 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 34.830 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.005 0.065 12755 Z= 0.246 Angle : 1.018 15.291 18477 Z= 0.559 Chirality : 0.053 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (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 HIS 0.013 0.002 HIS F 76 PHE 0.058 0.004 PHE A 67 TYR 0.058 0.004 TYR B 89 ARG 0.012 0.001 ARG G 89 Details of bonding type rmsd hydrogen bonds : bond 0.10902 ( 741) hydrogen bonds : angle 5.14104 ( 1855) covalent geometry : bond 0.00532 (12755) covalent geometry : angle 1.01789 (18477) *********************** 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 : 0.851 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: 0.5256 (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: 0.7253 (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 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: 0.8036 (ptp90) REVERT: C 42 GLN cc_start: 0.7677 (pp30) cc_final: 0.7306 (pp30) 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: 0.8415 (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: 0.8620 (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: 0.8405 (mm) REVERT: E 61 LEU cc_start: 0.8695 (mt) cc_final: 0.8265 (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: 0.7089 (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: 0.8488 (mtm-85) REVERT: G 21 LYS cc_start: 0.8733 (tmtt) cc_final: 0.8198 (tptt) REVERT: G 57 GLU cc_start: 0.8197 (tt0) cc_final: 0.7859 (tt0) REVERT: G 69 ASN cc_start: 0.8717 (m-40) cc_final: 0.8442 (m-40) REVERT: G 86 LEU cc_start: 0.9019 (mt) cc_final: 0.8656 (mt) REVERT: G 93 GLU cc_start: 0.8111 (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: 0.8997 (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: 0.7373 (t0) REVERT: H 55 THR cc_start: 0.8821 (m) cc_final: 0.8425 (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: 0.8136 (m90) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.3642 time to fit residues: 151.5623 Evaluate side-chains 212 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 108 ASN G 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.075483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053459 restraints weight = 65762.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.054445 restraints weight = 36071.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.055107 restraints weight = 25632.887| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12755 Z= 0.184 Angle : 0.635 8.591 18477 Z= 0.373 Chirality : 0.036 0.147 2105 Planarity : 0.005 0.053 1327 Dihedral : 31.620 177.500 4019 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.32 % Allowed : 5.73 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.29), residues: 738 helix: 0.11 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.22 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS F 76 PHE 0.023 0.002 PHE H 73 TYR 0.035 0.002 TYR H 86 ARG 0.012 0.001 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 741) hydrogen bonds : angle 3.34225 ( 1855) covalent geometry : bond 0.00403 (12755) covalent geometry : angle 0.63546 (18477) *********************** 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 244 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8558 (t80) cc_final: 0.8161 (t80) REVERT: A 73 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7324 (tm-30) REVERT: A 97 GLU cc_start: 0.8412 (pp20) cc_final: 0.8172 (pp20) REVERT: A 105 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 80 LYS cc_start: 0.8656 (pttm) cc_final: 0.7780 (ttmm) REVERT: B 85 MET cc_start: 0.7902 (mmm) cc_final: 0.6990 (mmm) REVERT: C 18 ARG cc_start: 0.8180 (ttt180) cc_final: 0.7758 (ttt180) REVERT: C 42 GLN cc_start: 0.7579 (pp30) cc_final: 0.6899 (pp30) REVERT: C 69 ASN cc_start: 0.8799 (m110) cc_final: 0.8594 (m110) REVERT: D 74 GLU cc_start: 0.8744 (pt0) cc_final: 0.8508 (pt0) REVERT: D 124 TYR cc_start: 0.8338 (t80) cc_final: 0.7401 (t80) REVERT: E 60 LEU cc_start: 0.8863 (mt) cc_final: 0.8628 (mp) REVERT: E 77 ASP cc_start: 0.8760 (p0) cc_final: 0.8361 (p0) REVERT: E 105 GLU cc_start: 0.8772 (tt0) cc_final: 0.8381 (tp30) REVERT: E 121 LYS cc_start: 0.9110 (ptmm) cc_final: 0.8892 (ptmt) REVERT: F 50 LEU cc_start: 0.8692 (pt) cc_final: 0.8118 (tt) REVERT: F 60 LYS cc_start: 0.8518 (mttt) cc_final: 0.7925 (mttt) REVERT: G 21 LYS cc_start: 0.9027 (tmtt) cc_final: 0.8589 (tptt) REVERT: G 74 ASN cc_start: 0.9038 (t0) cc_final: 0.8660 (t0) REVERT: G 93 GLU cc_start: 0.7531 (pt0) cc_final: 0.6955 (pt0) REVERT: H 48 LEU cc_start: 0.9491 (pt) cc_final: 0.9047 (tp) REVERT: H 79 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8630 (tp30) REVERT: H 119 ARG cc_start: 0.8617 (ppt170) cc_final: 0.8147 (ptm-80) outliers start: 2 outliers final: 0 residues processed: 243 average time/residue: 0.3405 time to fit residues: 108.1617 Evaluate side-chains 187 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 93 GLN C 39 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN D 112 HIS E 68 GLN E 93 GLN F 65 ASN F 76 HIS G 105 GLN H 50 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.072088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.049185 restraints weight = 65304.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.050103 restraints weight = 36280.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.050692 restraints weight = 26280.421| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12755 Z= 0.244 Angle : 0.678 6.901 18477 Z= 0.394 Chirality : 0.039 0.159 2105 Planarity : 0.005 0.056 1327 Dihedral : 31.831 177.076 4019 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.32 % Allowed : 7.17 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.30), residues: 738 helix: 0.80 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -1.18 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 76 PHE 0.016 0.003 PHE G 26 TYR 0.030 0.003 TYR D 86 ARG 0.006 0.001 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 741) hydrogen bonds : angle 3.28395 ( 1855) covalent geometry : bond 0.00546 (12755) covalent geometry : angle 0.67806 (18477) *********************** 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 235 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8042 (mp0) cc_final: 0.7826 (mp0) REVERT: A 94 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7781 (tt0) REVERT: A 105 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 54 GLU cc_start: 0.8731 (pp20) cc_final: 0.8379 (pp20) REVERT: B 60 LYS cc_start: 0.9127 (ttpp) cc_final: 0.8680 (ttpp) REVERT: B 64 GLU cc_start: 0.8854 (pm20) cc_final: 0.8622 (pm20) REVERT: B 85 MET cc_start: 0.8110 (mmm) cc_final: 0.7616 (mmm) REVERT: D 79 GLU cc_start: 0.8717 (tp30) cc_final: 0.8403 (tp30) REVERT: D 109 LEU cc_start: 0.9063 (mp) cc_final: 0.8685 (mt) REVERT: D 124 TYR cc_start: 0.8564 (t80) cc_final: 0.8026 (t80) REVERT: E 59 GLU cc_start: 0.8292 (tp30) cc_final: 0.7736 (pp20) REVERT: E 60 LEU cc_start: 0.8690 (mt) cc_final: 0.8188 (mm) REVERT: E 61 LEU cc_start: 0.8614 (mt) cc_final: 0.8153 (mt) REVERT: E 68 GLN cc_start: 0.8726 (tm130) cc_final: 0.8408 (tm-30) REVERT: E 77 ASP cc_start: 0.8585 (p0) cc_final: 0.8346 (p0) REVERT: E 78 PHE cc_start: 0.8029 (m-10) cc_final: 0.7679 (m-10) REVERT: E 105 GLU cc_start: 0.8759 (tt0) cc_final: 0.8401 (tp30) REVERT: F 60 LYS cc_start: 0.8621 (mttm) cc_final: 0.8034 (mttt) REVERT: F 75 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8030 (tm-30) REVERT: G 21 LYS cc_start: 0.9151 (tmtt) cc_final: 0.8696 (tptt) REVERT: G 42 GLN cc_start: 0.8665 (mp-120) cc_final: 0.8458 (mm-40) REVERT: G 72 ARG cc_start: 0.8488 (tpp80) cc_final: 0.8099 (mmt-90) REVERT: G 74 ASN cc_start: 0.9036 (t0) cc_final: 0.8757 (t0) REVERT: G 91 ASP cc_start: 0.8982 (t0) cc_final: 0.8705 (t0) REVERT: G 93 GLU cc_start: 0.7764 (pt0) cc_final: 0.7058 (pt0) REVERT: H 36 ARG cc_start: 0.7710 (tpp-160) cc_final: 0.7494 (tpp-160) REVERT: H 89 LYS cc_start: 0.8677 (tppt) cc_final: 0.8430 (mmtt) outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 0.4502 time to fit residues: 136.0101 Evaluate side-chains 176 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 68 GLN F 94 GLN G 114 GLN H 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.072727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.050231 restraints weight = 63637.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.051123 restraints weight = 35120.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.051715 restraints weight = 25117.457| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12755 Z= 0.185 Angle : 0.620 6.469 18477 Z= 0.363 Chirality : 0.036 0.150 2105 Planarity : 0.005 0.056 1327 Dihedral : 31.596 177.211 4019 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.30), residues: 738 helix: 1.30 (0.23), residues: 512 sheet: None (None), residues: 0 loop : -1.27 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 76 PHE 0.017 0.002 PHE C 26 TYR 0.036 0.002 TYR D 86 ARG 0.010 0.001 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 741) hydrogen bonds : angle 3.07088 ( 1855) covalent geometry : bond 0.00411 (12755) covalent geometry : angle 0.61979 (18477) *********************** 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 231 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7972 (mt-10) REVERT: A 76 GLN cc_start: 0.8741 (pm20) cc_final: 0.8490 (pm20) REVERT: A 105 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 60 LYS cc_start: 0.9089 (ttpp) cc_final: 0.8376 (ttpp) REVERT: B 64 GLU cc_start: 0.8863 (pm20) cc_final: 0.8265 (pm20) REVERT: B 80 LYS cc_start: 0.8665 (pttm) cc_final: 0.8126 (pttm) REVERT: B 85 MET cc_start: 0.7880 (mmm) cc_final: 0.7440 (mmm) REVERT: D 38 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7058 (pt0) REVERT: D 86 TYR cc_start: 0.8778 (m-80) cc_final: 0.8174 (m-80) REVERT: E 53 ARG cc_start: 0.8826 (tmt170) cc_final: 0.8335 (tmm-80) REVERT: E 61 LEU cc_start: 0.8708 (mt) cc_final: 0.8458 (mt) REVERT: E 68 GLN cc_start: 0.8641 (tm130) cc_final: 0.8406 (tm-30) REVERT: E 78 PHE cc_start: 0.8119 (m-10) cc_final: 0.7795 (m-10) REVERT: E 105 GLU cc_start: 0.8870 (tt0) cc_final: 0.8384 (tp30) REVERT: E 122 LYS cc_start: 0.9426 (ptmt) cc_final: 0.9167 (ptmm) REVERT: F 60 LYS cc_start: 0.8492 (mttm) cc_final: 0.7436 (mttt) REVERT: F 75 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7965 (tm-30) REVERT: G 21 LYS cc_start: 0.9034 (tttt) cc_final: 0.8542 (tptt) REVERT: G 42 GLN cc_start: 0.8714 (mp-120) cc_final: 0.8080 (mp10) REVERT: G 74 ASN cc_start: 0.9036 (t0) cc_final: 0.8759 (t0) REVERT: G 93 GLU cc_start: 0.7826 (pt0) cc_final: 0.6765 (pt0) REVERT: H 36 ARG cc_start: 0.7217 (tpp-160) cc_final: 0.6521 (tpp80) REVERT: H 57 ILE cc_start: 0.9071 (mm) cc_final: 0.8863 (mm) REVERT: H 108 GLU cc_start: 0.8169 (pm20) cc_final: 0.7838 (pm20) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3103 time to fit residues: 94.4098 Evaluate side-chains 189 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN F 94 GLN G 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.071005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.048437 restraints weight = 64198.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.049341 restraints weight = 35225.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.049918 restraints weight = 25339.877| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12755 Z= 0.244 Angle : 0.664 6.427 18477 Z= 0.387 Chirality : 0.039 0.183 2105 Planarity : 0.005 0.057 1327 Dihedral : 31.912 177.451 4019 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.31), residues: 738 helix: 1.19 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.29 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 76 PHE 0.017 0.003 PHE C 26 TYR 0.040 0.003 TYR H 86 ARG 0.008 0.001 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.04883 ( 741) hydrogen bonds : angle 3.29017 ( 1855) covalent geometry : bond 0.00545 (12755) covalent geometry : angle 0.66353 (18477) *********************** 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 224 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8094 (mt-10) REVERT: A 76 GLN cc_start: 0.8883 (pm20) cc_final: 0.8564 (pm20) REVERT: A 93 GLN cc_start: 0.9078 (mm110) cc_final: 0.8865 (mm110) REVERT: A 97 GLU cc_start: 0.8388 (pp20) cc_final: 0.8061 (pp20) REVERT: A 105 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7972 (tm-30) REVERT: B 54 GLU cc_start: 0.8641 (pp20) cc_final: 0.8400 (pp20) REVERT: B 80 LYS cc_start: 0.8745 (pttm) cc_final: 0.8279 (pttm) REVERT: B 89 TYR cc_start: 0.8644 (m-10) cc_final: 0.8274 (m-10) REVERT: C 57 GLU cc_start: 0.9002 (tt0) cc_final: 0.8797 (tt0) REVERT: D 38 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7039 (pt0) REVERT: D 51 THR cc_start: 0.8604 (t) cc_final: 0.8383 (t) REVERT: D 54 ASP cc_start: 0.8818 (p0) cc_final: 0.8409 (p0) REVERT: D 86 TYR cc_start: 0.8797 (m-80) cc_final: 0.8174 (m-80) REVERT: E 54 PHE cc_start: 0.8978 (m-80) cc_final: 0.8752 (m-10) REVERT: E 59 GLU cc_start: 0.8285 (tp30) cc_final: 0.7795 (pp20) REVERT: E 60 LEU cc_start: 0.8580 (mt) cc_final: 0.8276 (mm) REVERT: E 61 LEU cc_start: 0.8717 (mt) cc_final: 0.8310 (mt) REVERT: E 68 GLN cc_start: 0.8620 (tm130) cc_final: 0.8226 (tm-30) REVERT: E 105 GLU cc_start: 0.8895 (tt0) cc_final: 0.8381 (tp30) REVERT: F 28 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7660 (mp10) REVERT: F 75 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8038 (tm-30) REVERT: G 21 LYS cc_start: 0.9099 (tttt) cc_final: 0.8660 (tptt) REVERT: G 74 ASN cc_start: 0.9095 (t0) cc_final: 0.8837 (t0) REVERT: G 91 ASP cc_start: 0.9481 (t70) cc_final: 0.8756 (t0) REVERT: G 93 GLU cc_start: 0.8015 (pt0) cc_final: 0.7219 (pt0) REVERT: G 94 LEU cc_start: 0.9551 (mm) cc_final: 0.9338 (mm) REVERT: H 71 ASP cc_start: 0.8958 (t70) cc_final: 0.8685 (t0) REVERT: H 86 TYR cc_start: 0.8307 (m-10) cc_final: 0.7108 (m-80) REVERT: H 116 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7999 (mm-30) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3386 time to fit residues: 98.2462 Evaluate side-chains 181 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.071882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.049566 restraints weight = 63139.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.050471 restraints weight = 34058.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.051046 restraints weight = 24421.679| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12755 Z= 0.196 Angle : 0.645 7.399 18477 Z= 0.373 Chirality : 0.037 0.151 2105 Planarity : 0.004 0.056 1327 Dihedral : 31.768 177.324 4019 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.32 % Allowed : 2.55 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.31), residues: 738 helix: 1.35 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -1.31 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 76 PHE 0.016 0.002 PHE C 26 TYR 0.034 0.002 TYR H 86 ARG 0.007 0.001 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 741) hydrogen bonds : angle 3.17038 ( 1855) covalent geometry : bond 0.00439 (12755) covalent geometry : angle 0.64499 (18477) *********************** 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 225 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8876 (t) cc_final: 0.8624 (t) REVERT: A 73 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8069 (mt-10) REVERT: A 76 GLN cc_start: 0.8895 (pm20) cc_final: 0.8531 (pm20) REVERT: A 105 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7946 (tm-30) REVERT: B 54 GLU cc_start: 0.8639 (pp20) cc_final: 0.8289 (pp20) REVERT: B 80 LYS cc_start: 0.8768 (pttm) cc_final: 0.8326 (pttm) REVERT: B 89 TYR cc_start: 0.8607 (m-10) cc_final: 0.8223 (m-10) REVERT: C 105 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7264 (mm-40) REVERT: D 38 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7080 (pt0) REVERT: D 54 ASP cc_start: 0.8801 (p0) cc_final: 0.8436 (p0) REVERT: D 86 TYR cc_start: 0.8763 (m-80) cc_final: 0.7996 (m-80) REVERT: E 68 GLN cc_start: 0.8594 (tm130) cc_final: 0.8220 (tm-30) REVERT: E 105 GLU cc_start: 0.8919 (tt0) cc_final: 0.8447 (tm-30) REVERT: E 120 GLN cc_start: 0.8884 (tt0) cc_final: 0.8630 (tt0) REVERT: F 28 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7525 (mp10) REVERT: F 75 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7971 (tm-30) REVERT: G 21 LYS cc_start: 0.8968 (tttm) cc_final: 0.8738 (tptt) REVERT: G 74 ASN cc_start: 0.9074 (t0) cc_final: 0.8852 (t0) REVERT: G 91 ASP cc_start: 0.9431 (t70) cc_final: 0.8747 (t0) REVERT: G 93 GLU cc_start: 0.7959 (pt0) cc_final: 0.7399 (pt0) REVERT: G 94 LEU cc_start: 0.9528 (mm) cc_final: 0.9312 (mm) REVERT: H 36 ARG cc_start: 0.7454 (tpp-160) cc_final: 0.6875 (tpp80) REVERT: H 71 ASP cc_start: 0.8938 (t70) cc_final: 0.8712 (t0) REVERT: H 86 TYR cc_start: 0.8391 (m-10) cc_final: 0.8082 (m-80) REVERT: H 116 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8018 (mm-30) outliers start: 2 outliers final: 1 residues processed: 223 average time/residue: 0.3158 time to fit residues: 92.0682 Evaluate side-chains 180 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN F 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.071907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.049884 restraints weight = 63047.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.050776 restraints weight = 33999.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051356 restraints weight = 24343.333| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12755 Z= 0.186 Angle : 0.637 8.948 18477 Z= 0.368 Chirality : 0.037 0.148 2105 Planarity : 0.005 0.057 1327 Dihedral : 31.737 176.519 4019 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.31), residues: 738 helix: 1.31 (0.23), residues: 529 sheet: None (None), residues: 0 loop : -1.32 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS G 32 PHE 0.019 0.002 PHE C 26 TYR 0.027 0.002 TYR H 86 ARG 0.006 0.001 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 741) hydrogen bonds : angle 3.18662 ( 1855) covalent geometry : bond 0.00419 (12755) covalent geometry : angle 0.63724 (18477) *********************** 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 220 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.8817 (t) cc_final: 0.8580 (t) REVERT: A 73 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7961 (mt-10) REVERT: A 76 GLN cc_start: 0.8822 (pm20) cc_final: 0.8439 (pm20) REVERT: A 105 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 64 GLU cc_start: 0.8960 (pm20) cc_final: 0.8694 (pm20) REVERT: B 80 LYS cc_start: 0.8783 (pttm) cc_final: 0.8300 (pttm) REVERT: B 89 TYR cc_start: 0.8621 (m-10) cc_final: 0.8015 (m-10) REVERT: C 111 ASN cc_start: 0.8701 (m110) cc_final: 0.8474 (m110) REVERT: D 38 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7078 (pt0) REVERT: D 54 ASP cc_start: 0.8736 (p0) cc_final: 0.8376 (p0) REVERT: D 86 TYR cc_start: 0.8719 (m-80) cc_final: 0.7896 (m-80) REVERT: E 68 GLN cc_start: 0.8466 (tm130) cc_final: 0.8233 (tm-30) REVERT: E 105 GLU cc_start: 0.8845 (tt0) cc_final: 0.8429 (tm-30) REVERT: E 120 GLN cc_start: 0.8859 (tt0) cc_final: 0.8598 (tt0) REVERT: F 28 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7540 (mp10) REVERT: F 68 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.8075 (mtm-85) REVERT: F 75 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7880 (tm-30) REVERT: G 21 LYS cc_start: 0.8945 (tttm) cc_final: 0.8629 (tptt) REVERT: G 74 ASN cc_start: 0.9127 (t0) cc_final: 0.8846 (t0) REVERT: G 91 ASP cc_start: 0.9394 (t70) cc_final: 0.8893 (t0) REVERT: G 93 GLU cc_start: 0.7789 (pt0) cc_final: 0.7219 (pt0) REVERT: G 96 LYS cc_start: 0.9313 (tppt) cc_final: 0.9087 (tppt) REVERT: G 113 HIS cc_start: 0.8983 (t-170) cc_final: 0.8778 (t-170) REVERT: H 36 ARG cc_start: 0.7151 (tpp-160) cc_final: 0.6907 (tpp80) REVERT: H 116 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7946 (mm-30) REVERT: H 123 LYS cc_start: 0.8881 (tptp) cc_final: 0.8634 (tmtt) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.3432 time to fit residues: 99.0948 Evaluate side-chains 187 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.071203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.049278 restraints weight = 63229.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.050177 restraints weight = 33997.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.050760 restraints weight = 24157.077| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12755 Z= 0.208 Angle : 0.662 9.306 18477 Z= 0.379 Chirality : 0.038 0.151 2105 Planarity : 0.005 0.054 1327 Dihedral : 31.857 176.523 4019 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.31), residues: 738 helix: 1.32 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.27 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS G 32 PHE 0.017 0.002 PHE C 26 TYR 0.052 0.003 TYR H 86 ARG 0.005 0.000 ARG F 68 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 741) hydrogen bonds : angle 3.27966 ( 1855) covalent geometry : bond 0.00466 (12755) covalent geometry : angle 0.66172 (18477) *********************** 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 217 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 64 GLU cc_start: 0.8989 (pm20) cc_final: 0.8572 (pm20) REVERT: B 80 LYS cc_start: 0.8860 (pttm) cc_final: 0.8280 (pttm) REVERT: B 89 TYR cc_start: 0.8631 (m-10) cc_final: 0.8238 (m-10) REVERT: D 38 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7100 (pt0) REVERT: D 54 ASP cc_start: 0.8684 (p0) cc_final: 0.8317 (p0) REVERT: D 71 ASP cc_start: 0.8888 (t70) cc_final: 0.8628 (t0) REVERT: D 79 GLU cc_start: 0.8980 (tp30) cc_final: 0.8775 (tp30) REVERT: D 86 TYR cc_start: 0.8734 (m-80) cc_final: 0.8158 (m-80) REVERT: D 124 TYR cc_start: 0.8421 (t80) cc_final: 0.8029 (t80) REVERT: E 68 GLN cc_start: 0.8425 (tm130) cc_final: 0.8201 (tm-30) REVERT: E 105 GLU cc_start: 0.8871 (tt0) cc_final: 0.8394 (tp30) REVERT: E 120 GLN cc_start: 0.8879 (tt0) cc_final: 0.8275 (mt0) REVERT: F 75 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7926 (tm-30) REVERT: G 21 LYS cc_start: 0.9004 (tttm) cc_final: 0.8746 (tptt) REVERT: G 91 ASP cc_start: 0.9405 (t70) cc_final: 0.8627 (t0) REVERT: G 93 GLU cc_start: 0.7776 (pt0) cc_final: 0.7356 (pt0) REVERT: G 94 LEU cc_start: 0.9535 (mm) cc_final: 0.9325 (mm) REVERT: G 113 HIS cc_start: 0.9007 (t-170) cc_final: 0.8806 (t-170) REVERT: H 36 ARG cc_start: 0.7152 (tpp-160) cc_final: 0.6567 (tpp80) REVERT: H 116 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7939 (mm-30) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.3569 time to fit residues: 101.4505 Evaluate side-chains 179 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.072854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.050599 restraints weight = 62818.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.051526 restraints weight = 34283.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052141 restraints weight = 24600.983| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12755 Z= 0.165 Angle : 0.643 9.886 18477 Z= 0.368 Chirality : 0.036 0.164 2105 Planarity : 0.004 0.056 1327 Dihedral : 31.626 177.184 4019 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.31), residues: 738 helix: 1.34 (0.23), residues: 527 sheet: None (None), residues: 0 loop : -1.25 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.002 HIS G 32 PHE 0.017 0.002 PHE C 26 TYR 0.029 0.002 TYR C 58 ARG 0.014 0.001 ARG F 93 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 741) hydrogen bonds : angle 3.23418 ( 1855) covalent geometry : bond 0.00365 (12755) covalent geometry : angle 0.64341 (18477) *********************** 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 220 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8214 (pp20) cc_final: 0.7587 (pp20) REVERT: A 105 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7824 (tm-30) REVERT: B 54 GLU cc_start: 0.8592 (pp20) cc_final: 0.8151 (pp20) REVERT: B 64 GLU cc_start: 0.8871 (pm20) cc_final: 0.8515 (pm20) REVERT: B 80 LYS cc_start: 0.8851 (pttm) cc_final: 0.8299 (pttm) REVERT: B 89 TYR cc_start: 0.8614 (m-10) cc_final: 0.7746 (m-10) REVERT: C 105 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7182 (mm-40) REVERT: C 111 ASN cc_start: 0.8640 (m110) cc_final: 0.8232 (m110) REVERT: D 38 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7197 (pt0) REVERT: D 54 ASP cc_start: 0.8719 (p0) cc_final: 0.8440 (p0) REVERT: D 71 ASP cc_start: 0.8890 (t70) cc_final: 0.8629 (t0) REVERT: D 86 TYR cc_start: 0.8700 (m-80) cc_final: 0.7721 (m-80) REVERT: D 124 TYR cc_start: 0.8405 (t80) cc_final: 0.7964 (t80) REVERT: E 68 GLN cc_start: 0.8327 (tm130) cc_final: 0.8112 (tm-30) REVERT: E 77 ASP cc_start: 0.8848 (p0) cc_final: 0.8604 (p0) REVERT: E 105 GLU cc_start: 0.8810 (tt0) cc_final: 0.8359 (tp30) REVERT: F 28 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7880 (mm-40) REVERT: F 54 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8254 (tm-30) REVERT: F 63 LEU cc_start: 0.9387 (pp) cc_final: 0.9118 (tt) REVERT: G 91 ASP cc_start: 0.9355 (t70) cc_final: 0.8181 (t0) REVERT: G 92 ASP cc_start: 0.8957 (p0) cc_final: 0.8564 (p0) REVERT: G 93 GLU cc_start: 0.7566 (pt0) cc_final: 0.7171 (pm20) REVERT: G 96 LYS cc_start: 0.9251 (tppt) cc_final: 0.8968 (mmmt) REVERT: H 116 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7956 (mm-30) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.3462 time to fit residues: 101.3002 Evaluate side-chains 176 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN E 68 GLN E 93 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.072555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.050309 restraints weight = 63513.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051211 restraints weight = 34908.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.051791 restraints weight = 25133.301| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12755 Z= 0.182 Angle : 0.659 10.560 18477 Z= 0.375 Chirality : 0.037 0.166 2105 Planarity : 0.005 0.054 1327 Dihedral : 31.699 176.014 4019 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.31), residues: 738 helix: 1.22 (0.23), residues: 527 sheet: None (None), residues: 0 loop : -1.26 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.002 HIS G 32 PHE 0.015 0.002 PHE C 26 TYR 0.032 0.003 TYR F 89 ARG 0.010 0.001 ARG F 93 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 741) hydrogen bonds : angle 3.32153 ( 1855) covalent geometry : bond 0.00408 (12755) covalent geometry : angle 0.65851 (18477) ********************** 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 218 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 54 GLU cc_start: 0.8535 (pp20) cc_final: 0.8288 (pp20) REVERT: B 64 GLU cc_start: 0.8880 (pm20) cc_final: 0.8515 (pm20) REVERT: B 80 LYS cc_start: 0.8866 (pttm) cc_final: 0.8274 (pttm) REVERT: D 38 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7178 (pt0) REVERT: D 54 ASP cc_start: 0.8692 (p0) cc_final: 0.8388 (p0) REVERT: D 71 ASP cc_start: 0.8950 (t70) cc_final: 0.8676 (t0) REVERT: D 86 TYR cc_start: 0.8662 (m-80) cc_final: 0.7634 (m-80) REVERT: D 124 TYR cc_start: 0.8422 (t80) cc_final: 0.7987 (t80) REVERT: E 68 GLN cc_start: 0.8343 (tm130) cc_final: 0.8119 (tm-30) REVERT: E 105 GLU cc_start: 0.8822 (tt0) cc_final: 0.8382 (tp30) REVERT: E 120 GLN cc_start: 0.8940 (tt0) cc_final: 0.8318 (mt0) REVERT: F 28 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7854 (mm-40) REVERT: F 54 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8115 (tm-30) REVERT: G 74 ASN cc_start: 0.9085 (t0) cc_final: 0.8872 (t0) REVERT: G 91 ASP cc_start: 0.9366 (t70) cc_final: 0.8345 (t0) REVERT: G 92 ASP cc_start: 0.8949 (p0) cc_final: 0.8532 (p0) REVERT: G 93 GLU cc_start: 0.7584 (pt0) cc_final: 0.7157 (pm20) REVERT: G 96 LYS cc_start: 0.9289 (tppt) cc_final: 0.8999 (mmmt) REVERT: G 113 HIS cc_start: 0.8966 (t-170) cc_final: 0.8606 (t-170) REVERT: H 71 ASP cc_start: 0.8897 (t70) cc_final: 0.8687 (t0) REVERT: H 86 TYR cc_start: 0.8213 (m-80) cc_final: 0.7185 (m-80) REVERT: H 116 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7999 (mm-30) REVERT: H 119 ARG cc_start: 0.8717 (ptm-80) cc_final: 0.8228 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3101 time to fit residues: 89.3698 Evaluate side-chains 178 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 67 optimal weight: 0.0470 chunk 36 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 94 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.073539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051138 restraints weight = 63250.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052078 restraints weight = 34753.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.052688 restraints weight = 24943.546| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12755 Z= 0.162 Angle : 0.642 10.240 18477 Z= 0.366 Chirality : 0.036 0.152 2105 Planarity : 0.004 0.056 1327 Dihedral : 31.525 176.808 4019 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.31), residues: 738 helix: 1.24 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.30 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS G 32 PHE 0.012 0.002 PHE C 26 TYR 0.025 0.002 TYR H 86 ARG 0.009 0.001 ARG F 68 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 741) hydrogen bonds : angle 3.18899 ( 1855) covalent geometry : bond 0.00359 (12755) covalent geometry : angle 0.64170 (18477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4246.23 seconds wall clock time: 76 minutes 14.06 seconds (4574.06 seconds total)