Starting phenix.real_space_refine on Tue Mar 3 14:35:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d74_46602/03_2026/9d74_46602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d74_46602/03_2026/9d74_46602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d74_46602/03_2026/9d74_46602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d74_46602/03_2026/9d74_46602.map" model { file = "/net/cci-nas-00/data/ceres_data/9d74_46602/03_2026/9d74_46602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d74_46602/03_2026/9d74_46602.cif" } resolution = 3.31 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= 0.001 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3794 2.51 5 N 1028 2.21 5 O 1171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6017 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2132 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 15, 'TRANS': 257} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 792 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 93} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1462 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 12, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 47 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1557 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 64 Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N PRO H 123 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO H 123 " occ=0.50 residue: pdb=" N LEU H 124 " occ=0.00 ... (3 atoms not shown) pdb=" CB LEU H 124 " occ=0.00 residue: pdb=" N ALA H 125 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA H 125 " occ=0.50 residue: pdb=" N PRO H 126 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO H 126 " occ=0.50 residue: pdb=" N THR H 135 " occ=0.50 ... (3 atoms not shown) pdb=" CB THR H 135 " occ=0.50 residue: pdb=" N ALA H 136 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA H 136 " occ=0.50 residue: pdb=" N LEU H 138 " occ=0.50 ... (3 atoms not shown) pdb=" CB LEU H 138 " occ=0.50 residue: pdb=" N GLY H 139 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY H 139 " occ=0.00 residue: pdb=" N PHE H 146 " occ=0.50 ... (3 atoms not shown) pdb=" CB PHE H 146 " occ=0.50 residue: pdb=" N THR H 191 " occ=0.00 ... (3 atoms not shown) pdb=" CB THR H 191 " occ=0.00 Time building chain proxies: 1.40, per 1000 atoms: 0.23 Number of scatterers: 6017 At special positions: 0 Unit cell: (70.55, 63.08, 147.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1171 8.00 N 1028 7.00 C 3794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 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: 0.50 Conformation dependent library (CDL) restraints added in 345.5 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 15 sheets defined 12.7% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.913A pdb=" N ILE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 86 removed outlier: 3.901A pdb=" N ARG A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 150 removed outlier: 4.248A pdb=" N THR A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 removed outlier: 4.052A pdb=" N GLN A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.801A pdb=" N LYS H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.829A pdb=" N SER H 91 " --> pdb=" O ASN H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 126 Processing helix chain 'L' and resid 182 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 3.612A pdb=" N GLU A 46 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG A 35 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP A 37 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE A 22 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR A 118 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 193 removed outlier: 5.755A pdb=" N PHE A 241 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 193 removed outlier: 5.755A pdb=" N PHE A 241 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 214 through 219 removed outlier: 4.084A pdb=" N CYS A 259 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 removed outlier: 6.254A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B 50 " --> pdb=" O TYR B 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 46 removed outlier: 4.687A pdb=" N LEU B 39 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.986A pdb=" N GLN H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.099A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 120 through 124 Processing sheet with id=AB1, first strand: chain 'H' and resid 150 through 154 Processing sheet with id=AB2, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.740A pdb=" N THR L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.841A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.841A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 113 through 117 removed outlier: 6.000A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 152 through 153 removed outlier: 3.525A pdb=" N ILE L 204 " --> pdb=" O ALA L 195 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1966 1.34 - 1.46: 1591 1.46 - 1.58: 2581 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 6172 Sorted by residual: bond pdb=" CB ASN B 83 " pdb=" CG ASN B 83 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CB THR A 73 " pdb=" CG2 THR A 73 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" CG1 ILE H 48 " pdb=" CD1 ILE H 48 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.04e+00 bond pdb=" CB GLU L 17 " pdb=" CG GLU L 17 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CB ILE A 66 " pdb=" CG2 ILE A 66 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.96e-01 ... (remaining 6167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 8315 2.41 - 4.82: 101 4.82 - 7.23: 7 7.23 - 9.64: 5 9.64 - 12.05: 1 Bond angle restraints: 8429 Sorted by residual: angle pdb=" CB MET L 105 " pdb=" CG MET L 105 " pdb=" SD MET L 105 " ideal model delta sigma weight residual 112.70 124.75 -12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CB LYS B 41 " pdb=" CG LYS B 41 " pdb=" CD LYS B 41 " ideal model delta sigma weight residual 111.30 118.65 -7.35 2.30e+00 1.89e-01 1.02e+01 angle pdb=" CA GLU L 17 " pdb=" CB GLU L 17 " pdb=" CG GLU L 17 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA LEU H 178 " pdb=" CB LEU H 178 " pdb=" CG LEU H 178 " ideal model delta sigma weight residual 116.30 125.49 -9.19 3.50e+00 8.16e-02 6.90e+00 angle pdb=" CB GLU L 17 " pdb=" CG GLU L 17 " pdb=" CD GLU L 17 " ideal model delta sigma weight residual 112.60 116.88 -4.28 1.70e+00 3.46e-01 6.35e+00 ... (remaining 8424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 3103 17.56 - 35.11: 403 35.11 - 52.67: 106 52.67 - 70.22: 14 70.22 - 87.78: 12 Dihedral angle restraints: 3638 sinusoidal: 1308 harmonic: 2330 Sorted by residual: dihedral pdb=" CB CYS H 140 " pdb=" SG CYS H 140 " pdb=" SG CYS H 196 " pdb=" CB CYS H 196 " ideal model delta sinusoidal sigma weight residual 93.00 163.86 -70.86 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CA ILE B 7 " pdb=" C ILE B 7 " pdb=" N GLN B 8 " pdb=" CA GLN B 8 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CB CYS L 133 " pdb=" SG CYS L 133 " pdb=" SG CYS L 193 " pdb=" CB CYS L 193 " ideal model delta sinusoidal sigma weight residual 93.00 58.44 34.56 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 3635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 609 0.034 - 0.067: 209 0.067 - 0.101: 78 0.101 - 0.135: 30 0.135 - 0.168: 3 Chirality restraints: 929 Sorted by residual: chirality pdb=" CG LEU H 11 " pdb=" CB LEU H 11 " pdb=" CD1 LEU H 11 " pdb=" CD2 LEU H 11 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA HIS B 31 " pdb=" N HIS B 31 " pdb=" C HIS B 31 " pdb=" CB HIS B 31 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE A 94 " pdb=" N ILE A 94 " pdb=" C ILE A 94 " pdb=" CB ILE A 94 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 926 not shown) Planarity restraints: 1093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 146 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO H 147 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 147 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 147 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU L 17 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" CD GLU L 17 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU L 17 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU L 17 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 7 " -0.015 2.00e-02 2.50e+03 1.25e-02 2.74e+00 pdb=" CG PHE P 7 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE P 7 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE P 7 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE P 7 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE P 7 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE P 7 " -0.002 2.00e-02 2.50e+03 ... (remaining 1090 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1132 2.76 - 3.30: 5881 3.30 - 3.83: 10322 3.83 - 4.37: 11473 4.37 - 4.90: 19792 Nonbonded interactions: 48600 Sorted by model distance: nonbonded pdb=" N ASP H 57 " pdb=" OD1 ASP H 57 " model vdw 2.229 3.120 nonbonded pdb=" O SER A 131 " pdb=" OG SER A 131 " model vdw 2.238 3.040 nonbonded pdb=" O SER L 77 " pdb=" OG SER L 77 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR A 143 " pdb=" O PHE P 9 " model vdw 2.249 3.040 nonbonded pdb=" O ARG H 13 " pdb=" OG SER H 16 " model vdw 2.257 3.040 ... (remaining 48595 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.180 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.004 0.040 6179 Z= 0.178 Angle : 0.683 12.049 8443 Z= 0.351 Chirality : 0.042 0.168 929 Planarity : 0.005 0.064 1093 Dihedral : 17.529 87.776 2125 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 6.59 % Allowed : 29.49 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.30), residues: 786 helix: -0.17 (0.61), residues: 75 sheet: -0.22 (0.29), residues: 326 loop : -1.05 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 5 TYR 0.019 0.002 TYR B 26 PHE 0.028 0.002 PHE P 7 TRP 0.023 0.002 TRP H 47 HIS 0.009 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 6172) covalent geometry : angle 0.68223 ( 8429) SS BOND : bond 0.00373 ( 7) SS BOND : angle 0.88699 ( 14) hydrogen bonds : bond 0.13396 ( 253) hydrogen bonds : angle 5.99913 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 86 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7564 (ttm) cc_final: 0.7154 (mtp) REVERT: A 44 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7915 (mtm110) REVERT: A 97 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8611 (ttt-90) REVERT: B 23 LEU cc_start: 0.7055 (mt) cc_final: 0.6640 (mt) REVERT: H 13 ARG cc_start: 0.9439 (tpp80) cc_final: 0.9186 (tpp80) REVERT: H 19 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7797 (tttp) REVERT: H 39 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: H 55 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8270 (p0) REVERT: L 39 LYS cc_start: 0.8747 (mptm) cc_final: 0.8390 (mptt) REVERT: L 85 ILE cc_start: 0.8842 (mm) cc_final: 0.8578 (mm) REVERT: L 106 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8460 (tptp) outliers start: 40 outliers final: 31 residues processed: 119 average time/residue: 0.0825 time to fit residues: 12.9082 Evaluate side-chains 121 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 142 ASP Chi-restraints excluded: chain L residue 143 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 93 HIS A 115 GLN A 262 GLN A 263 HIS B 21 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN H 164 HIS L 30 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.117183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.085801 restraints weight = 16945.393| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 4.71 r_work: 0.3466 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6179 Z= 0.155 Angle : 0.629 7.965 8443 Z= 0.317 Chirality : 0.042 0.161 929 Planarity : 0.004 0.060 1093 Dihedral : 8.655 59.535 944 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 6.75 % Allowed : 27.68 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.30), residues: 786 helix: -0.26 (0.57), residues: 84 sheet: -0.17 (0.29), residues: 326 loop : -1.05 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 5 TYR 0.018 0.002 TYR L 91 PHE 0.021 0.001 PHE P 7 TRP 0.015 0.001 TRP H 47 HIS 0.009 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6172) covalent geometry : angle 0.62809 ( 8429) SS BOND : bond 0.00363 ( 7) SS BOND : angle 1.02311 ( 14) hydrogen bonds : bond 0.03460 ( 253) hydrogen bonds : angle 5.03706 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7803 (ttm) cc_final: 0.6878 (mtp) REVERT: A 21 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7621 (ttt-90) REVERT: A 46 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6357 (pm20) REVERT: A 197 HIS cc_start: 0.8869 (t70) cc_final: 0.8580 (t70) REVERT: B 23 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7216 (mt) REVERT: H 13 ARG cc_start: 0.9327 (tpp80) cc_final: 0.9058 (tpp80) REVERT: H 19 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7987 (tttt) REVERT: H 55 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.7990 (p0) REVERT: L 39 LYS cc_start: 0.8503 (mptm) cc_final: 0.8161 (mptt) REVERT: L 82 ASP cc_start: 0.7872 (p0) cc_final: 0.7587 (p0) REVERT: L 85 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8293 (mm) REVERT: L 105 MET cc_start: 0.8830 (mmm) cc_final: 0.8311 (mmm) outliers start: 41 outliers final: 28 residues processed: 121 average time/residue: 0.0721 time to fit residues: 11.7882 Evaluate side-chains 116 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 135 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 37 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 76 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.118966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.086859 restraints weight = 16694.519| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 4.84 r_work: 0.3461 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6179 Z= 0.119 Angle : 0.598 9.162 8443 Z= 0.297 Chirality : 0.041 0.160 929 Planarity : 0.004 0.059 1093 Dihedral : 7.179 57.901 903 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.17 % Rotamer: Outliers : 6.92 % Allowed : 27.68 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.30), residues: 786 helix: -0.13 (0.57), residues: 84 sheet: -0.06 (0.29), residues: 330 loop : -0.96 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 5 TYR 0.013 0.001 TYR L 91 PHE 0.016 0.001 PHE P 7 TRP 0.012 0.001 TRP H 47 HIS 0.007 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6172) covalent geometry : angle 0.59764 ( 8429) SS BOND : bond 0.00390 ( 7) SS BOND : angle 0.90600 ( 14) hydrogen bonds : bond 0.03142 ( 253) hydrogen bonds : angle 4.73481 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6417 (pm20) REVERT: A 197 HIS cc_start: 0.8885 (t70) cc_final: 0.8683 (t70) REVERT: B 23 LEU cc_start: 0.7666 (mt) cc_final: 0.7348 (mt) REVERT: B 63 TYR cc_start: 0.8308 (p90) cc_final: 0.8107 (p90) REVERT: H 19 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7977 (tttt) REVERT: H 29 PHE cc_start: 0.8364 (t80) cc_final: 0.8126 (t80) REVERT: H 55 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8378 (p0) REVERT: H 89 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8596 (tm-30) REVERT: L 39 LYS cc_start: 0.8422 (mptm) cc_final: 0.8121 (mptt) REVERT: L 82 ASP cc_start: 0.7833 (p0) cc_final: 0.7619 (p0) REVERT: L 85 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8280 (mm) REVERT: L 104 GLU cc_start: 0.7970 (mp0) cc_final: 0.7572 (mp0) REVERT: L 105 MET cc_start: 0.8859 (mmm) cc_final: 0.8317 (mmm) outliers start: 42 outliers final: 30 residues processed: 128 average time/residue: 0.0668 time to fit residues: 11.6432 Evaluate side-chains 118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 205 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN L 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.118994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.086618 restraints weight = 16681.630| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 4.90 r_work: 0.3464 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6179 Z= 0.112 Angle : 0.588 8.787 8443 Z= 0.293 Chirality : 0.041 0.159 929 Planarity : 0.004 0.058 1093 Dihedral : 7.063 56.506 903 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 7.25 % Allowed : 26.85 % Favored : 65.90 % 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: -0.74 (0.30), residues: 786 helix: -0.21 (0.57), residues: 84 sheet: 0.01 (0.29), residues: 329 loop : -0.95 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 5 TYR 0.013 0.001 TYR L 91 PHE 0.014 0.001 PHE P 7 TRP 0.030 0.002 TRP H 33 HIS 0.005 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6172) covalent geometry : angle 0.58780 ( 8429) SS BOND : bond 0.00377 ( 7) SS BOND : angle 0.88062 ( 14) hydrogen bonds : bond 0.03004 ( 253) hydrogen bonds : angle 4.60317 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6302 (pm20) REVERT: A 197 HIS cc_start: 0.8892 (t70) cc_final: 0.8661 (t70) REVERT: B 23 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7364 (mt) REVERT: H 19 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7958 (tttt) REVERT: H 29 PHE cc_start: 0.8360 (t80) cc_final: 0.8114 (t80) REVERT: H 55 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8347 (p0) REVERT: H 89 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8780 (tm-30) REVERT: L 39 LYS cc_start: 0.8393 (mptm) cc_final: 0.8137 (mptt) REVERT: L 85 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8280 (mm) REVERT: L 105 MET cc_start: 0.8841 (mmm) cc_final: 0.8283 (mmm) outliers start: 44 outliers final: 27 residues processed: 130 average time/residue: 0.0633 time to fit residues: 11.2302 Evaluate side-chains 119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 181 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN H 43 GLN L 30 ASN ** L 90 GLN ** 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 = 0.4098 r_free = 0.4098 target = 0.112584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.082280 restraints weight = 17395.996| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.65 r_work: 0.3413 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6179 Z= 0.158 Angle : 0.626 8.409 8443 Z= 0.315 Chirality : 0.042 0.162 929 Planarity : 0.004 0.059 1093 Dihedral : 7.047 55.496 901 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 7.08 % Allowed : 27.02 % Favored : 65.90 % 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: -0.78 (0.30), residues: 786 helix: -0.37 (0.56), residues: 86 sheet: -0.05 (0.29), residues: 333 loop : -0.92 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.019 0.002 TYR L 91 PHE 0.012 0.001 PHE H 29 TRP 0.021 0.001 TRP H 33 HIS 0.007 0.001 HIS H 200 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6172) covalent geometry : angle 0.62482 ( 8429) SS BOND : bond 0.00423 ( 7) SS BOND : angle 0.96638 ( 14) hydrogen bonds : bond 0.03169 ( 253) hydrogen bonds : angle 4.71005 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 89 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6362 (pm20) REVERT: A 197 HIS cc_start: 0.8898 (t70) cc_final: 0.8671 (t70) REVERT: B 23 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7338 (mt) REVERT: H 19 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8001 (tttp) REVERT: H 29 PHE cc_start: 0.8543 (t80) cc_final: 0.8318 (t80) REVERT: H 89 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8766 (tm-30) REVERT: L 39 LYS cc_start: 0.8498 (mptm) cc_final: 0.8216 (mptt) REVERT: L 85 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8413 (mm) REVERT: L 105 MET cc_start: 0.8850 (mmm) cc_final: 0.8279 (mmm) outliers start: 43 outliers final: 35 residues processed: 126 average time/residue: 0.0710 time to fit residues: 12.3532 Evaluate side-chains 123 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 84 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 181 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 48 optimal weight: 20.0000 chunk 4 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN H 6 GLN H 43 GLN L 30 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.118347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.086802 restraints weight = 16847.951| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 4.86 r_work: 0.3441 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6179 Z= 0.128 Angle : 0.609 9.153 8443 Z= 0.304 Chirality : 0.042 0.160 929 Planarity : 0.004 0.057 1093 Dihedral : 6.901 58.273 901 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer: Outliers : 7.41 % Allowed : 27.02 % Favored : 65.57 % 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: -0.65 (0.30), residues: 786 helix: -0.21 (0.56), residues: 86 sheet: 0.13 (0.29), residues: 329 loop : -0.94 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 5 TYR 0.018 0.002 TYR A 113 PHE 0.017 0.001 PHE P 7 TRP 0.018 0.001 TRP H 33 HIS 0.007 0.001 HIS H 200 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6172) covalent geometry : angle 0.60861 ( 8429) SS BOND : bond 0.00385 ( 7) SS BOND : angle 0.87904 ( 14) hydrogen bonds : bond 0.02984 ( 253) hydrogen bonds : angle 4.59902 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 89 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.5016 (tmm-80) REVERT: A 46 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6126 (pm20) REVERT: A 197 HIS cc_start: 0.8948 (t70) cc_final: 0.8649 (t70) REVERT: B 8 GLN cc_start: 0.7284 (mp10) cc_final: 0.6831 (pm20) REVERT: H 19 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8008 (tttt) REVERT: H 29 PHE cc_start: 0.8554 (t80) cc_final: 0.8335 (t80) REVERT: H 89 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8766 (tm-30) REVERT: L 39 LYS cc_start: 0.8418 (mptm) cc_final: 0.8209 (mptt) REVERT: L 85 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8257 (mm) REVERT: L 104 GLU cc_start: 0.7842 (mp0) cc_final: 0.7585 (mp0) REVERT: L 105 MET cc_start: 0.8821 (mmm) cc_final: 0.8312 (mmm) outliers start: 45 outliers final: 33 residues processed: 126 average time/residue: 0.0665 time to fit residues: 11.3370 Evaluate side-chains 123 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 181 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 0.0170 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 74 optimal weight: 40.0000 chunk 33 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 70 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.7776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN H 43 GLN L 30 ASN ** L 90 GLN ** 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 = 0.4136 r_free = 0.4136 target = 0.111405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.083212 restraints weight = 16835.420| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 4.45 r_work: 0.3497 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6179 Z= 0.111 Angle : 0.603 8.761 8443 Z= 0.299 Chirality : 0.041 0.158 929 Planarity : 0.004 0.055 1093 Dihedral : 6.734 58.606 901 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.17 % Rotamer: Outliers : 6.43 % Allowed : 29.00 % Favored : 64.58 % 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: -0.53 (0.30), residues: 786 helix: -0.04 (0.56), residues: 86 sheet: 0.25 (0.29), residues: 327 loop : -0.93 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 5 TYR 0.017 0.001 TYR A 113 PHE 0.025 0.001 PHE P 7 TRP 0.023 0.001 TRP H 47 HIS 0.005 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6172) covalent geometry : angle 0.60254 ( 8429) SS BOND : bond 0.00367 ( 7) SS BOND : angle 0.81199 ( 14) hydrogen bonds : bond 0.02893 ( 253) hydrogen bonds : angle 4.51665 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7936 (ttm) cc_final: 0.7166 (mtp) REVERT: A 46 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6481 (pm20) REVERT: A 197 HIS cc_start: 0.8794 (t70) cc_final: 0.8475 (t70) REVERT: B 8 GLN cc_start: 0.7616 (mp10) cc_final: 0.7236 (pm20) REVERT: H 6 GLN cc_start: 0.7331 (mt0) cc_final: 0.7087 (mt0) REVERT: H 19 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8122 (tttt) REVERT: H 29 PHE cc_start: 0.8390 (t80) cc_final: 0.8159 (t80) REVERT: H 89 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8750 (tm-30) REVERT: L 39 LYS cc_start: 0.8563 (mptm) cc_final: 0.8339 (mptt) REVERT: L 85 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8547 (mm) REVERT: L 104 GLU cc_start: 0.7871 (mp0) cc_final: 0.7528 (mp0) outliers start: 39 outliers final: 31 residues processed: 121 average time/residue: 0.0705 time to fit residues: 11.6598 Evaluate side-chains 120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 181 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN H 43 GLN H 77 ASN L 30 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.110469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.082197 restraints weight = 17101.698| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 4.46 r_work: 0.3449 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6179 Z= 0.135 Angle : 0.618 8.601 8443 Z= 0.308 Chirality : 0.042 0.159 929 Planarity : 0.004 0.055 1093 Dihedral : 6.730 56.937 898 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.53 % Rotamer: Outliers : 6.26 % Allowed : 29.32 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.30), residues: 786 helix: 0.06 (0.56), residues: 86 sheet: 0.23 (0.29), residues: 327 loop : -0.89 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.017 0.002 TYR B 63 PHE 0.026 0.002 PHE P 7 TRP 0.016 0.001 TRP H 47 HIS 0.005 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6172) covalent geometry : angle 0.61753 ( 8429) SS BOND : bond 0.00374 ( 7) SS BOND : angle 0.97856 ( 14) hydrogen bonds : bond 0.02991 ( 253) hydrogen bonds : angle 4.55519 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7942 (ttm) cc_final: 0.7125 (mtp) REVERT: A 46 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6424 (pm20) REVERT: A 197 HIS cc_start: 0.8888 (t70) cc_final: 0.8584 (t70) REVERT: B 8 GLN cc_start: 0.7537 (mp10) cc_final: 0.7151 (pm20) REVERT: H 6 GLN cc_start: 0.7361 (mt0) cc_final: 0.7130 (mt0) REVERT: H 19 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7960 (tttp) REVERT: H 29 PHE cc_start: 0.8535 (t80) cc_final: 0.8318 (t80) REVERT: H 89 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8766 (tm-30) REVERT: L 39 LYS cc_start: 0.8449 (mptm) cc_final: 0.8229 (mptt) REVERT: L 85 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8399 (mm) outliers start: 38 outliers final: 32 residues processed: 119 average time/residue: 0.0694 time to fit residues: 11.3362 Evaluate side-chains 120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 181 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN H 43 GLN L 30 ASN ** L 90 GLN ** 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 = 0.4114 r_free = 0.4114 target = 0.110294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.082005 restraints weight = 17058.065| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 4.47 r_work: 0.3461 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6179 Z= 0.130 Angle : 0.616 9.325 8443 Z= 0.305 Chirality : 0.042 0.159 929 Planarity : 0.004 0.055 1093 Dihedral : 6.633 56.745 898 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.17 % Rotamer: Outliers : 6.26 % Allowed : 29.00 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.30), residues: 786 helix: 0.18 (0.57), residues: 86 sheet: 0.25 (0.29), residues: 327 loop : -0.90 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 5 TYR 0.013 0.001 TYR A 113 PHE 0.023 0.001 PHE P 7 TRP 0.015 0.001 TRP H 47 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6172) covalent geometry : angle 0.61515 ( 8429) SS BOND : bond 0.00356 ( 7) SS BOND : angle 0.92481 ( 14) hydrogen bonds : bond 0.02940 ( 253) hydrogen bonds : angle 4.48928 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 85 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7972 (ttm) cc_final: 0.7176 (mtp) REVERT: A 46 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6460 (pm20) REVERT: A 197 HIS cc_start: 0.8836 (t70) cc_final: 0.8534 (t70) REVERT: B 8 GLN cc_start: 0.7654 (mp10) cc_final: 0.7299 (pm20) REVERT: B 67 TYR cc_start: 0.8684 (p90) cc_final: 0.8466 (p90) REVERT: H 6 GLN cc_start: 0.7372 (mt0) cc_final: 0.7141 (mt0) REVERT: H 19 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8095 (tttt) REVERT: H 89 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8746 (tm-30) REVERT: L 85 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8495 (mm) REVERT: L 104 GLU cc_start: 0.7838 (mp0) cc_final: 0.7511 (mp0) REVERT: L 105 MET cc_start: 0.8822 (mmm) cc_final: 0.8126 (mmm) outliers start: 38 outliers final: 32 residues processed: 117 average time/residue: 0.0689 time to fit residues: 11.1640 Evaluate side-chains 119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 181 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN H 43 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.107848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.079252 restraints weight = 16801.093| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 4.57 r_work: 0.3373 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6179 Z= 0.169 Angle : 0.636 9.426 8443 Z= 0.319 Chirality : 0.042 0.163 929 Planarity : 0.004 0.055 1093 Dihedral : 6.776 59.700 898 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.85 % Favored : 94.02 % Rotamer: Outliers : 6.26 % Allowed : 29.00 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.30), residues: 786 helix: 0.19 (0.57), residues: 86 sheet: 0.11 (0.29), residues: 333 loop : -0.86 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 111 TYR 0.020 0.002 TYR L 91 PHE 0.026 0.002 PHE P 7 TRP 0.015 0.001 TRP H 33 HIS 0.006 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6172) covalent geometry : angle 0.63482 ( 8429) SS BOND : bond 0.00400 ( 7) SS BOND : angle 1.01400 ( 14) hydrogen bonds : bond 0.03126 ( 253) hydrogen bonds : angle 4.62764 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 84 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6044 (pm20) REVERT: A 197 HIS cc_start: 0.9055 (t70) cc_final: 0.8787 (t70) REVERT: H 6 GLN cc_start: 0.7220 (mt0) cc_final: 0.6984 (mt0) REVERT: H 19 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7705 (tttp) REVERT: H 89 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8734 (tm-30) REVERT: L 85 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8048 (mm) REVERT: L 105 MET cc_start: 0.8705 (mmm) cc_final: 0.8158 (mmm) outliers start: 38 outliers final: 32 residues processed: 117 average time/residue: 0.0711 time to fit residues: 11.4025 Evaluate side-chains 117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 181 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN L 30 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.117654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.086597 restraints weight = 16961.705| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 4.74 r_work: 0.3488 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6179 Z= 0.115 Angle : 0.620 9.280 8443 Z= 0.307 Chirality : 0.041 0.158 929 Planarity : 0.004 0.054 1093 Dihedral : 6.414 56.080 898 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.33 % Favored : 95.55 % Rotamer: Outliers : 5.11 % Allowed : 29.98 % Favored : 64.91 % 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: -0.44 (0.30), residues: 786 helix: 0.31 (0.57), residues: 86 sheet: 0.27 (0.29), residues: 327 loop : -0.90 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 5 TYR 0.012 0.001 TYR A 113 PHE 0.021 0.001 PHE P 7 TRP 0.019 0.001 TRP H 47 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6172) covalent geometry : angle 0.61923 ( 8429) SS BOND : bond 0.00339 ( 7) SS BOND : angle 0.86985 ( 14) hydrogen bonds : bond 0.02876 ( 253) hydrogen bonds : angle 4.47790 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1805.76 seconds wall clock time: 31 minutes 35.17 seconds (1895.17 seconds total)