Starting phenix.real_space_refine on Wed Sep 17 13:49:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddq_46780/09_2025/9ddq_46780.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddq_46780/09_2025/9ddq_46780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ddq_46780/09_2025/9ddq_46780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddq_46780/09_2025/9ddq_46780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ddq_46780/09_2025/9ddq_46780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddq_46780/09_2025/9ddq_46780.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 37 5.16 5 C 5790 2.51 5 N 1574 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9069 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1695 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "B" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1705 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "C" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1702 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1695 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "E" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1702 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "F" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 120 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "Y" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 229 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "Z" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 221 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 26} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.29, per 1000 atoms: 0.25 Number of scatterers: 9069 At special positions: 0 Unit cell: (83.83, 83.83, 119.52, 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 37 16.00 O 1668 8.00 N 1574 7.00 C 5790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 267.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 0 sheets defined 90.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 Processing helix chain 'A' and resid 20 through 63 removed outlier: 3.626A pdb=" N VAL A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 103 through 127 Processing helix chain 'A' and resid 129 through 161 removed outlier: 3.640A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.638A pdb=" N VAL A 169 " --> pdb=" O ASN A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 170 through 231 removed outlier: 3.896A pdb=" N ALA A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Proline residue: A 190 - end of helix Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 20 through 63 removed outlier: 4.014A pdb=" N GLU B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 76 Processing helix chain 'B' and resid 82 through 97 Processing helix chain 'B' and resid 103 through 127 removed outlier: 4.000A pdb=" N ILE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 163 removed outlier: 3.880A pdb=" N LEU B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 166 through 233 removed outlier: 3.863A pdb=" N VAL B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) Proline residue: B 172 - end of helix Proline residue: B 190 - end of helix Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 20 through 63 Processing helix chain 'C' and resid 67 through 76 Processing helix chain 'C' and resid 82 through 98 Processing helix chain 'C' and resid 103 through 127 Processing helix chain 'C' and resid 129 through 163 removed outlier: 4.099A pdb=" N LEU C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) Proline residue: C 141 - end of helix removed outlier: 4.241A pdb=" N GLY C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 233 removed outlier: 4.036A pdb=" N VAL C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Proline residue: C 172 - end of helix removed outlier: 3.743A pdb=" N ALA C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Proline residue: C 190 - end of helix Processing helix chain 'D' and resid 11 through 19 Processing helix chain 'D' and resid 20 through 63 removed outlier: 3.918A pdb=" N GLU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN D 50 " --> pdb=" O VAL D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 76 Processing helix chain 'D' and resid 82 through 97 Processing helix chain 'D' and resid 103 through 127 Processing helix chain 'D' and resid 129 through 161 removed outlier: 3.678A pdb=" N LEU D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) Proline residue: D 141 - end of helix removed outlier: 3.515A pdb=" N GLN D 161 " --> pdb=" O ILE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 230 removed outlier: 3.570A pdb=" N VAL D 170 " --> pdb=" O ASN D 166 " (cutoff:3.500A) Proline residue: D 172 - end of helix removed outlier: 3.732A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Proline residue: D 190 - end of helix Processing helix chain 'E' and resid 11 through 19 removed outlier: 3.514A pdb=" N TYR E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 63 Processing helix chain 'E' and resid 67 through 76 Processing helix chain 'E' and resid 82 through 98 removed outlier: 3.600A pdb=" N LEU E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 127 removed outlier: 3.512A pdb=" N GLY E 127 " --> pdb=" O GLY E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 163 removed outlier: 3.996A pdb=" N LEU E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) Proline residue: E 141 - end of helix Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 169 through 230 removed outlier: 4.430A pdb=" N GLY E 173 " --> pdb=" O VAL E 169 " (cutoff:3.500A) Proline residue: E 190 - end of helix Processing helix chain 'F' and resid 11 through 25 removed outlier: 3.699A pdb=" N ALA F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 20 through 41 Proline residue: Y 39 - end of helix Processing helix chain 'Z' and resid 21 through 38 removed outlier: 4.117A pdb=" N ASP Z 25 " --> pdb=" O THR Z 21 " (cutoff:3.500A) 847 hydrogen bonds defined for protein. 2541 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: 1.10 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2535 1.33 - 1.45: 1360 1.45 - 1.58: 5240 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 9203 Sorted by residual: bond pdb=" N HIS Z 16 " pdb=" CA HIS Z 16 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.06e-02 8.90e+03 1.20e+01 bond pdb=" N VAL B 169 " pdb=" CA VAL B 169 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N VAL D 186 " pdb=" CA VAL D 186 " ideal model delta sigma weight residual 1.459 1.501 -0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" C CYS C 25 " pdb=" N VAL C 26 " ideal model delta sigma weight residual 1.334 1.373 -0.039 1.25e-02 6.40e+03 9.68e+00 bond pdb=" N VAL C 143 " pdb=" CA VAL C 143 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.43e+00 ... (remaining 9198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 7901 1.39 - 2.79: 3494 2.79 - 4.18: 942 4.18 - 5.57: 112 5.57 - 6.97: 13 Bond angle restraints: 12462 Sorted by residual: angle pdb=" OE1 GLN C 17 " pdb=" CD GLN C 17 " pdb=" NE2 GLN C 17 " ideal model delta sigma weight residual 122.60 118.60 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" CB HIS B 233 " pdb=" CG HIS B 233 " pdb=" CD2 HIS B 233 " ideal model delta sigma weight residual 131.20 126.02 5.18 1.30e+00 5.92e-01 1.59e+01 angle pdb=" OE1 GLN E 125 " pdb=" CD GLN E 125 " pdb=" NE2 GLN E 125 " ideal model delta sigma weight residual 122.60 118.64 3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" CD ARG D 118 " pdb=" NE ARG D 118 " pdb=" CZ ARG D 118 " ideal model delta sigma weight residual 124.40 129.92 -5.52 1.40e+00 5.10e-01 1.55e+01 angle pdb=" CA PHE E 48 " pdb=" CB PHE E 48 " pdb=" CG PHE E 48 " ideal model delta sigma weight residual 113.80 109.87 3.93 1.00e+00 1.00e+00 1.55e+01 ... (remaining 12457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5025 17.53 - 35.06: 349 35.06 - 52.59: 63 52.59 - 70.12: 27 70.12 - 87.65: 6 Dihedral angle restraints: 5470 sinusoidal: 2064 harmonic: 3406 Sorted by residual: dihedral pdb=" CG ARG D 54 " pdb=" CD ARG D 54 " pdb=" NE ARG D 54 " pdb=" CZ ARG D 54 " ideal model delta sinusoidal sigma weight residual 90.00 2.35 87.65 2 1.50e+01 4.44e-03 2.13e+01 dihedral pdb=" CA ILE Z 18 " pdb=" C ILE Z 18 " pdb=" N ASN Z 19 " pdb=" CA ASN Z 19 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" C LYS B 81 " pdb=" N LYS B 81 " pdb=" CA LYS B 81 " pdb=" CB LYS B 81 " ideal model delta harmonic sigma weight residual -122.60 -132.20 9.60 0 2.50e+00 1.60e-01 1.47e+01 ... (remaining 5467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1056 0.085 - 0.170: 360 0.170 - 0.255: 50 0.255 - 0.340: 10 0.340 - 0.425: 2 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CG LEU A 10 " pdb=" CB LEU A 10 " pdb=" CD1 LEU A 10 " pdb=" CD2 LEU A 10 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA SER C 140 " pdb=" N SER C 140 " pdb=" C SER C 140 " pdb=" CB SER C 140 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA LEU D 167 " pdb=" N LEU D 167 " pdb=" C LEU D 167 " pdb=" CB LEU D 167 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 1475 not shown) Planarity restraints: 1600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 16 " 0.105 2.00e-02 2.50e+03 5.46e-02 5.95e+01 pdb=" CG TYR D 16 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 16 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR D 16 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR D 16 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR D 16 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR D 16 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR D 16 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 16 " 0.096 2.00e-02 2.50e+03 5.05e-02 5.11e+01 pdb=" CG TYR C 16 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR C 16 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR C 16 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR C 16 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR C 16 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR C 16 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 16 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 13 " 0.091 2.00e-02 2.50e+03 4.41e-02 4.85e+01 pdb=" CG TRP B 13 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 13 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 13 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 13 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP B 13 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 13 " -0.052 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 13 " 0.053 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 13 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP B 13 " 0.040 2.00e-02 2.50e+03 ... (remaining 1597 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 2808 2.87 - 3.38: 10246 3.38 - 3.89: 15287 3.89 - 4.39: 15517 4.39 - 4.90: 28383 Nonbonded interactions: 72241 Sorted by model distance: nonbonded pdb=" CG ARG D 54 " pdb=" NH1 ARG D 54 " model vdw 2.368 3.520 nonbonded pdb=" O ALA C 232 " pdb=" C HIS C 233 " model vdw 2.441 3.270 nonbonded pdb=" O GLN A 161 " pdb=" C THR A 162 " model vdw 2.466 3.270 nonbonded pdb=" O ALA C 160 " pdb=" NE2 GLN C 163 " model vdw 2.505 3.120 nonbonded pdb=" OG1 THR D 181 " pdb=" OD2 ASP Z 25 " model vdw 2.513 3.040 ... (remaining 72236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 9 and (name N or name CA or name C or name O or name CB ) \ ) or resid 10 through 232)) selection = (chain 'B' and ((resid 9 and (name N or name CA or name C or name O or name CB ) \ ) or resid 10 through 232)) selection = (chain 'C' and resid 9 through 232) selection = (chain 'D' and ((resid 9 and (name N or name CA or name C or name O or name CB ) \ ) or resid 10 through 232)) selection = (chain 'E' and ((resid 9 and (name N or name CA or name C or name O or name CB ) \ ) or resid 10 through 232)) } ncs_group { reference = (chain 'Y' and (resid 12 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )))) selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.750 Find NCS groups from input model: 0.140 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 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 : 0.011 0.041 9203 Z= 0.687 Angle : 1.593 6.966 12462 Z= 1.113 Chirality : 0.083 0.425 1478 Planarity : 0.014 0.121 1600 Dihedral : 13.661 87.649 3270 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.75 % Allowed : 8.12 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.22), residues: 1183 helix: 0.45 (0.14), residues: 1048 sheet: None (None), residues: 0 loop : -0.55 (0.56), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 110 TYR 0.105 0.018 TYR D 16 PHE 0.070 0.010 PHE E 48 TRP 0.091 0.017 TRP B 13 HIS 0.013 0.002 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.01090 ( 9203) covalent geometry : angle 1.59269 (12462) hydrogen bonds : bond 0.14735 ( 847) hydrogen bonds : angle 6.38537 ( 2541) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 385 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.8475 (t-90) cc_final: 0.7939 (t-170) REVERT: A 24 LYS cc_start: 0.8869 (mttm) cc_final: 0.8247 (mmtm) REVERT: A 27 MET cc_start: 0.8876 (mmt) cc_final: 0.7737 (mpp) REVERT: A 32 LEU cc_start: 0.9723 (mt) cc_final: 0.9519 (mp) REVERT: A 81 LYS cc_start: 0.9393 (mmtt) cc_final: 0.9071 (mtpt) REVERT: A 89 ASN cc_start: 0.9200 (m110) cc_final: 0.8841 (m110) REVERT: A 104 ASN cc_start: 0.9339 (m-40) cc_final: 0.9101 (m110) REVERT: A 105 GLU cc_start: 0.8898 (mp0) cc_final: 0.8673 (mm-30) REVERT: A 109 GLU cc_start: 0.9042 (tp30) cc_final: 0.8840 (tp30) REVERT: A 154 ASN cc_start: 0.8541 (m-40) cc_final: 0.8320 (m110) REVERT: A 161 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7181 (mm-40) REVERT: A 229 SER cc_start: 0.8759 (t) cc_final: 0.8533 (p) REVERT: B 13 TRP cc_start: 0.8853 (t-100) cc_final: 0.8497 (t-100) REVERT: B 20 ASP cc_start: 0.9083 (t70) cc_final: 0.8747 (t70) REVERT: B 25 CYS cc_start: 0.9205 (t) cc_final: 0.8822 (m) REVERT: B 27 MET cc_start: 0.9075 (mmm) cc_final: 0.8844 (mmm) REVERT: B 69 ASN cc_start: 0.8977 (t0) cc_final: 0.8470 (t0) REVERT: B 72 ASN cc_start: 0.9383 (m-40) cc_final: 0.8966 (m110) REVERT: B 86 HIS cc_start: 0.8575 (t-170) cc_final: 0.8163 (t70) REVERT: B 89 ASN cc_start: 0.9201 (m110) cc_final: 0.8841 (m110) REVERT: B 90 GLU cc_start: 0.8860 (tp30) cc_final: 0.8471 (tp30) REVERT: B 93 ASN cc_start: 0.9402 (t0) cc_final: 0.9168 (t0) REVERT: B 94 GLU cc_start: 0.9147 (tp30) cc_final: 0.8612 (tp30) REVERT: B 104 ASN cc_start: 0.8933 (m110) cc_final: 0.8691 (m-40) REVERT: B 116 GLU cc_start: 0.8969 (tt0) cc_final: 0.8623 (tt0) REVERT: B 130 ASN cc_start: 0.8957 (m-40) cc_final: 0.8697 (m110) REVERT: C 44 LYS cc_start: 0.9324 (mmmm) cc_final: 0.9050 (mmtt) REVERT: C 47 GLU cc_start: 0.9172 (tp30) cc_final: 0.8901 (tp30) REVERT: C 64 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8448 (tm-30) REVERT: C 70 GLN cc_start: 0.8820 (tt0) cc_final: 0.8468 (tt0) REVERT: C 84 SER cc_start: 0.9299 (p) cc_final: 0.8737 (p) REVERT: C 89 ASN cc_start: 0.9389 (m-40) cc_final: 0.9144 (m110) REVERT: C 92 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8526 (tm-30) REVERT: C 96 GLU cc_start: 0.9103 (pt0) cc_final: 0.8662 (pt0) REVERT: C 223 ASP cc_start: 0.9007 (m-30) cc_final: 0.8767 (m-30) REVERT: C 227 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8563 (tm-30) REVERT: D 20 ASP cc_start: 0.9211 (t0) cc_final: 0.8959 (t70) REVERT: D 58 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8857 (mm-30) REVERT: D 89 ASN cc_start: 0.8972 (p0) cc_final: 0.8682 (p0) REVERT: D 90 GLU cc_start: 0.8915 (tt0) cc_final: 0.8611 (tt0) REVERT: D 219 LEU cc_start: 0.9409 (mt) cc_final: 0.9012 (mt) REVERT: E 13 TRP cc_start: 0.8957 (t-100) cc_final: 0.8659 (t-100) REVERT: E 103 ASP cc_start: 0.9226 (t0) cc_final: 0.9014 (t0) REVERT: E 109 GLU cc_start: 0.9065 (tp30) cc_final: 0.8660 (tp30) REVERT: E 166 ASN cc_start: 0.9054 (t0) cc_final: 0.8796 (t0) REVERT: E 176 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8485 (mt-10) REVERT: E 211 ASP cc_start: 0.9216 (t0) cc_final: 0.8912 (t0) REVERT: Z 26 VAL cc_start: 0.9801 (t) cc_final: 0.9588 (m) outliers start: 7 outliers final: 1 residues processed: 389 average time/residue: 0.0841 time to fit residues: 45.3124 Evaluate side-chains 302 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN B 89 ASN B 166 ASN D 72 ASN E 18 HIS E 130 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.056889 restraints weight = 23402.894| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.38 r_work: 0.2743 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9203 Z= 0.163 Angle : 0.615 11.919 12462 Z= 0.321 Chirality : 0.039 0.169 1478 Planarity : 0.003 0.033 1600 Dihedral : 4.133 34.953 1267 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 3.53 % Allowed : 15.38 % Favored : 81.09 % 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 aren not related in a simple way. whole: 3.40 (0.24), residues: 1183 helix: 2.50 (0.15), residues: 1053 sheet: None (None), residues: 0 loop : 0.09 (0.62), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 117 TYR 0.013 0.002 TYR E 195 PHE 0.018 0.002 PHE D 49 TRP 0.020 0.002 TRP A 13 HIS 0.010 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9203) covalent geometry : angle 0.61458 (12462) hydrogen bonds : bond 0.04871 ( 847) hydrogen bonds : angle 3.78098 ( 2541) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 309 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.9185 (mtp) cc_final: 0.8890 (mtp) REVERT: A 18 HIS cc_start: 0.8865 (t-90) cc_final: 0.8451 (t-170) REVERT: A 89 ASN cc_start: 0.9049 (m-40) cc_final: 0.8618 (m110) REVERT: A 109 GLU cc_start: 0.8985 (tp30) cc_final: 0.8566 (tp30) REVERT: A 154 ASN cc_start: 0.8477 (m-40) cc_final: 0.8207 (m-40) REVERT: B 13 TRP cc_start: 0.8761 (t-100) cc_final: 0.8545 (t60) REVERT: B 20 ASP cc_start: 0.8961 (t70) cc_final: 0.8726 (t70) REVERT: B 25 CYS cc_start: 0.9186 (t) cc_final: 0.8946 (m) REVERT: B 27 MET cc_start: 0.9169 (mmm) cc_final: 0.8900 (mmm) REVERT: B 47 GLU cc_start: 0.9087 (tp30) cc_final: 0.8746 (tm-30) REVERT: B 72 ASN cc_start: 0.9396 (m-40) cc_final: 0.9132 (m110) REVERT: B 86 HIS cc_start: 0.8724 (t-170) cc_final: 0.8460 (t-170) REVERT: B 93 ASN cc_start: 0.9366 (t0) cc_final: 0.9158 (t0) REVERT: B 104 ASN cc_start: 0.9097 (m110) cc_final: 0.8851 (m-40) REVERT: B 105 GLU cc_start: 0.8887 (tp30) cc_final: 0.8318 (tp30) REVERT: B 116 GLU cc_start: 0.9239 (tt0) cc_final: 0.8956 (tt0) REVERT: B 223 ASP cc_start: 0.9372 (t0) cc_final: 0.9044 (t0) REVERT: B 227 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8710 (mt-10) REVERT: C 44 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8924 (mmtt) REVERT: C 64 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8574 (tm-30) REVERT: C 85 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9433 (tm) REVERT: C 96 GLU cc_start: 0.8967 (pt0) cc_final: 0.8470 (pt0) REVERT: C 102 ASP cc_start: 0.9226 (p0) cc_final: 0.8978 (p0) REVERT: C 164 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8353 (t) REVERT: C 166 ASN cc_start: 0.8772 (t0) cc_final: 0.8413 (t0) REVERT: C 176 GLU cc_start: 0.9198 (tt0) cc_final: 0.8893 (tt0) REVERT: C 211 ASP cc_start: 0.9390 (t0) cc_final: 0.9036 (t0) REVERT: C 223 ASP cc_start: 0.9037 (m-30) cc_final: 0.8757 (m-30) REVERT: D 20 ASP cc_start: 0.9102 (t0) cc_final: 0.8884 (t70) REVERT: E 13 TRP cc_start: 0.8818 (t-100) cc_final: 0.8617 (t-100) REVERT: E 108 LYS cc_start: 0.9049 (mtpt) cc_final: 0.8787 (mtpt) REVERT: E 109 GLU cc_start: 0.9156 (tp30) cc_final: 0.8832 (tp30) REVERT: E 166 ASN cc_start: 0.8941 (t0) cc_final: 0.8639 (t0) REVERT: E 176 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8568 (mt-10) REVERT: Y 27 MET cc_start: 0.9147 (mmt) cc_final: 0.8930 (mmt) outliers start: 33 outliers final: 15 residues processed: 320 average time/residue: 0.0814 time to fit residues: 36.7882 Evaluate side-chains 302 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 285 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 13 TRP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 22 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 GLN B 51 GLN B 69 ASN B 130 ASN C 89 ASN D 72 ASN E 104 ASN E 130 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.071121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.055785 restraints weight = 23370.232| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.33 r_work: 0.2721 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9203 Z= 0.200 Angle : 0.597 8.084 12462 Z= 0.309 Chirality : 0.039 0.174 1478 Planarity : 0.003 0.023 1600 Dihedral : 3.719 28.858 1267 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 4.49 % Allowed : 18.38 % Favored : 77.14 % 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 aren not related in a simple way. whole: 3.92 (0.24), residues: 1183 helix: 2.87 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -0.16 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.016 0.002 TYR B 16 PHE 0.012 0.001 PHE D 49 TRP 0.011 0.001 TRP A 13 HIS 0.004 0.001 HIS F 20 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9203) covalent geometry : angle 0.59698 (12462) hydrogen bonds : bond 0.04440 ( 847) hydrogen bonds : angle 3.59500 ( 2541) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.9131 (mtp) cc_final: 0.8900 (mtp) REVERT: A 16 TYR cc_start: 0.9421 (t80) cc_final: 0.9033 (t80) REVERT: A 18 HIS cc_start: 0.8847 (t-90) cc_final: 0.8086 (t-170) REVERT: A 24 LYS cc_start: 0.8649 (mttm) cc_final: 0.8424 (mmtm) REVERT: A 58 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8828 (tt0) REVERT: A 89 ASN cc_start: 0.9046 (m-40) cc_final: 0.8706 (m110) REVERT: A 90 GLU cc_start: 0.8790 (tp30) cc_final: 0.8359 (tp30) REVERT: A 109 GLU cc_start: 0.8966 (tp30) cc_final: 0.8525 (tp30) REVERT: A 176 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8394 (mt-10) REVERT: B 20 ASP cc_start: 0.8914 (t70) cc_final: 0.8605 (t70) REVERT: B 25 CYS cc_start: 0.9159 (t) cc_final: 0.8928 (m) REVERT: B 72 ASN cc_start: 0.9425 (m-40) cc_final: 0.9171 (m110) REVERT: B 86 HIS cc_start: 0.8637 (t-170) cc_final: 0.8263 (t-170) REVERT: B 90 GLU cc_start: 0.8819 (tp30) cc_final: 0.8494 (tp30) REVERT: B 93 ASN cc_start: 0.9341 (t0) cc_final: 0.9115 (t0) REVERT: B 94 GLU cc_start: 0.9302 (tp30) cc_final: 0.8894 (tp30) REVERT: B 104 ASN cc_start: 0.9064 (m110) cc_final: 0.8810 (m-40) REVERT: B 105 GLU cc_start: 0.8664 (tp30) cc_final: 0.8414 (tp30) REVERT: B 116 GLU cc_start: 0.9258 (tt0) cc_final: 0.8985 (tt0) REVERT: B 208 MET cc_start: 0.9169 (tpp) cc_final: 0.8931 (tpt) REVERT: B 223 ASP cc_start: 0.9341 (t0) cc_final: 0.8978 (t0) REVERT: B 227 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8589 (mt-10) REVERT: C 24 LYS cc_start: 0.8982 (mttm) cc_final: 0.8767 (mmtt) REVERT: C 102 ASP cc_start: 0.9215 (p0) cc_final: 0.8974 (p0) REVERT: C 109 GLU cc_start: 0.9037 (tp30) cc_final: 0.8707 (tp30) REVERT: C 164 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8485 (t) REVERT: C 211 ASP cc_start: 0.9406 (t0) cc_final: 0.9073 (t0) REVERT: C 223 ASP cc_start: 0.9067 (m-30) cc_final: 0.8796 (m-30) REVERT: E 108 LYS cc_start: 0.9119 (mtpt) cc_final: 0.8874 (mtpt) REVERT: E 109 GLU cc_start: 0.9127 (tp30) cc_final: 0.8662 (tp30) REVERT: E 164 THR cc_start: 0.9330 (t) cc_final: 0.9106 (p) REVERT: E 166 ASN cc_start: 0.8947 (t0) cc_final: 0.8685 (t0) REVERT: E 176 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8498 (mt-10) outliers start: 42 outliers final: 24 residues processed: 304 average time/residue: 0.0792 time to fit residues: 34.1533 Evaluate side-chains 297 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 13 TRP Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain Y residue 17 ASP Chi-restraints excluded: chain Y residue 23 PHE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Z residue 19 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 0.1980 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 154 ASN B 69 ASN B 130 ASN C 89 ASN D 18 HIS D 92 GLN E 104 ASN ** F 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.071971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.056617 restraints weight = 23612.268| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.32 r_work: 0.2743 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9203 Z= 0.151 Angle : 0.564 8.806 12462 Z= 0.291 Chirality : 0.037 0.195 1478 Planarity : 0.003 0.021 1600 Dihedral : 3.581 24.413 1267 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 4.27 % Allowed : 18.59 % Favored : 77.14 % 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 aren not related in a simple way. whole: 4.14 (0.24), residues: 1183 helix: 3.02 (0.15), residues: 1059 sheet: None (None), residues: 0 loop : -0.20 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.016 0.002 TYR B 16 PHE 0.018 0.001 PHE C 205 TRP 0.009 0.001 TRP A 13 HIS 0.008 0.001 HIS F 20 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9203) covalent geometry : angle 0.56445 (12462) hydrogen bonds : bond 0.04170 ( 847) hydrogen bonds : angle 3.46576 ( 2541) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 295 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.9415 (t80) cc_final: 0.9124 (t80) REVERT: A 18 HIS cc_start: 0.8872 (t-90) cc_final: 0.8012 (t-170) REVERT: A 85 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8618 (tm) REVERT: A 89 ASN cc_start: 0.9030 (m-40) cc_final: 0.8620 (m-40) REVERT: A 90 GLU cc_start: 0.8794 (tp30) cc_final: 0.8588 (tp30) REVERT: A 109 GLU cc_start: 0.8940 (tp30) cc_final: 0.8498 (tp30) REVERT: A 176 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8422 (mt-10) REVERT: B 20 ASP cc_start: 0.8886 (t70) cc_final: 0.8542 (t70) REVERT: B 25 CYS cc_start: 0.9112 (t) cc_final: 0.8892 (m) REVERT: B 47 GLU cc_start: 0.9103 (tp30) cc_final: 0.8710 (tm-30) REVERT: B 72 ASN cc_start: 0.9427 (m-40) cc_final: 0.9185 (m-40) REVERT: B 86 HIS cc_start: 0.8633 (t-170) cc_final: 0.8303 (t-170) REVERT: B 90 GLU cc_start: 0.8749 (tp30) cc_final: 0.8314 (tp30) REVERT: B 116 GLU cc_start: 0.9281 (tt0) cc_final: 0.9003 (tt0) REVERT: B 208 MET cc_start: 0.9159 (tpp) cc_final: 0.8917 (tpt) REVERT: B 223 ASP cc_start: 0.9336 (t0) cc_final: 0.8958 (t0) REVERT: B 227 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8544 (mt-10) REVERT: C 102 ASP cc_start: 0.9196 (p0) cc_final: 0.8968 (p0) REVERT: C 109 GLU cc_start: 0.9000 (tp30) cc_final: 0.8582 (tp30) REVERT: C 211 ASP cc_start: 0.9379 (t0) cc_final: 0.9066 (t0) REVERT: C 223 ASP cc_start: 0.9064 (m-30) cc_final: 0.8781 (m-30) REVERT: D 109 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8811 (mp0) REVERT: E 108 LYS cc_start: 0.9113 (mtpt) cc_final: 0.8872 (mtpt) REVERT: E 109 GLU cc_start: 0.9071 (tp30) cc_final: 0.8675 (tp30) REVERT: E 164 THR cc_start: 0.9314 (t) cc_final: 0.9044 (p) REVERT: E 166 ASN cc_start: 0.8969 (t0) cc_final: 0.8692 (t0) REVERT: F 20 HIS cc_start: 0.7939 (m170) cc_final: 0.7729 (m170) outliers start: 40 outliers final: 28 residues processed: 312 average time/residue: 0.0793 time to fit residues: 35.0533 Evaluate side-chains 310 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 281 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Z residue 19 ASN Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 25 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 5.9990 chunk 103 optimal weight: 0.0470 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN B 130 ASN ** F 20 HIS ** 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 = 0.3239 r_free = 0.3239 target = 0.071894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.056468 restraints weight = 23606.430| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.39 r_work: 0.2734 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9203 Z= 0.160 Angle : 0.579 8.491 12462 Z= 0.298 Chirality : 0.038 0.199 1478 Planarity : 0.003 0.022 1600 Dihedral : 3.461 16.393 1266 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 4.38 % Allowed : 18.80 % Favored : 76.82 % 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 aren not related in a simple way. whole: 4.20 (0.24), residues: 1183 helix: 3.06 (0.15), residues: 1057 sheet: None (None), residues: 0 loop : -0.12 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 114 TYR 0.017 0.002 TYR B 16 PHE 0.016 0.001 PHE B 198 TRP 0.015 0.001 TRP E 13 HIS 0.003 0.001 HIS F 20 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9203) covalent geometry : angle 0.57864 (12462) hydrogen bonds : bond 0.04096 ( 847) hydrogen bonds : angle 3.50250 ( 2541) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 293 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.8834 (t-90) cc_final: 0.7958 (t-170) REVERT: A 85 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8817 (tm) REVERT: A 89 ASN cc_start: 0.9040 (m-40) cc_final: 0.8774 (m-40) REVERT: A 90 GLU cc_start: 0.8795 (tp30) cc_final: 0.8412 (tp30) REVERT: A 109 GLU cc_start: 0.8951 (tp30) cc_final: 0.8503 (tp30) REVERT: A 176 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8435 (mt-10) REVERT: B 20 ASP cc_start: 0.8900 (t70) cc_final: 0.8547 (t70) REVERT: B 25 CYS cc_start: 0.9117 (t) cc_final: 0.8885 (m) REVERT: B 47 GLU cc_start: 0.9134 (tp30) cc_final: 0.8733 (tm-30) REVERT: B 86 HIS cc_start: 0.8597 (t-170) cc_final: 0.8311 (t-170) REVERT: B 90 GLU cc_start: 0.8674 (tp30) cc_final: 0.8399 (tp30) REVERT: B 116 GLU cc_start: 0.9293 (tt0) cc_final: 0.9006 (tt0) REVERT: B 208 MET cc_start: 0.9164 (tpp) cc_final: 0.8920 (tpt) REVERT: B 223 ASP cc_start: 0.9333 (t0) cc_final: 0.8942 (t0) REVERT: B 227 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8503 (mt-10) REVERT: C 86 HIS cc_start: 0.8799 (t-90) cc_final: 0.8514 (t70) REVERT: C 102 ASP cc_start: 0.9186 (p0) cc_final: 0.8960 (p0) REVERT: C 109 GLU cc_start: 0.8988 (tp30) cc_final: 0.8525 (tp30) REVERT: C 211 ASP cc_start: 0.9406 (t0) cc_final: 0.9108 (t0) REVERT: C 223 ASP cc_start: 0.9087 (m-30) cc_final: 0.8790 (m-30) REVERT: D 154 ASN cc_start: 0.9117 (m-40) cc_final: 0.8877 (m110) REVERT: E 94 GLU cc_start: 0.9562 (tp30) cc_final: 0.8798 (tp30) REVERT: E 108 LYS cc_start: 0.9117 (mtpt) cc_final: 0.8875 (mtpt) REVERT: E 109 GLU cc_start: 0.9063 (tp30) cc_final: 0.8645 (tp30) REVERT: E 164 THR cc_start: 0.9310 (t) cc_final: 0.9011 (p) REVERT: E 166 ASN cc_start: 0.8970 (t0) cc_final: 0.8723 (t0) REVERT: E 176 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8884 (mm-30) REVERT: F 20 HIS cc_start: 0.7986 (m170) cc_final: 0.7748 (m170) REVERT: Y 15 MET cc_start: 0.8207 (mmm) cc_final: 0.7305 (mtm) outliers start: 41 outliers final: 32 residues processed: 314 average time/residue: 0.0780 time to fit residues: 34.8992 Evaluate side-chains 302 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain Y residue 17 ASP Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Z residue 19 ASN Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 34 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.073792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.058310 restraints weight = 23415.180| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.37 r_work: 0.2774 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9203 Z= 0.140 Angle : 0.589 8.946 12462 Z= 0.301 Chirality : 0.038 0.222 1478 Planarity : 0.003 0.024 1600 Dihedral : 3.442 16.467 1266 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 4.27 % Allowed : 20.51 % Favored : 75.21 % 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 aren not related in a simple way. whole: 4.14 (0.24), residues: 1183 helix: 3.02 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -0.16 (0.60), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.019 0.001 TYR B 16 PHE 0.012 0.001 PHE B 113 TRP 0.019 0.001 TRP E 13 HIS 0.002 0.001 HIS F 20 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9203) covalent geometry : angle 0.58928 (12462) hydrogen bonds : bond 0.03996 ( 847) hydrogen bonds : angle 3.49839 ( 2541) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 291 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 18 HIS cc_start: 0.8829 (t-90) cc_final: 0.7932 (t-170) REVERT: A 85 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8696 (tm) REVERT: A 89 ASN cc_start: 0.9047 (m-40) cc_final: 0.8702 (m110) REVERT: A 90 GLU cc_start: 0.8738 (tp30) cc_final: 0.8367 (tp30) REVERT: A 109 GLU cc_start: 0.8905 (tp30) cc_final: 0.8497 (tp30) REVERT: A 176 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8419 (mt-10) REVERT: B 20 ASP cc_start: 0.8920 (t70) cc_final: 0.8685 (t70) REVERT: B 89 ASN cc_start: 0.9204 (m-40) cc_final: 0.8795 (m110) REVERT: B 116 GLU cc_start: 0.9310 (tt0) cc_final: 0.9030 (tt0) REVERT: B 208 MET cc_start: 0.9136 (tpp) cc_final: 0.8881 (tpt) REVERT: B 218 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9194 (mm) REVERT: C 86 HIS cc_start: 0.8732 (t-90) cc_final: 0.8428 (t70) REVERT: C 89 ASN cc_start: 0.9291 (m-40) cc_final: 0.8965 (m110) REVERT: C 102 ASP cc_start: 0.9160 (p0) cc_final: 0.8952 (p0) REVERT: C 176 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8762 (tt0) REVERT: C 211 ASP cc_start: 0.9377 (t0) cc_final: 0.9107 (t0) REVERT: C 223 ASP cc_start: 0.9049 (m-30) cc_final: 0.8759 (m-30) REVERT: D 109 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8858 (mp0) REVERT: D 154 ASN cc_start: 0.9159 (m-40) cc_final: 0.8887 (m110) REVERT: E 108 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8908 (mtpt) REVERT: E 109 GLU cc_start: 0.8988 (tp30) cc_final: 0.8603 (tp30) REVERT: E 164 THR cc_start: 0.9239 (t) cc_final: 0.8943 (p) REVERT: E 166 ASN cc_start: 0.8979 (t0) cc_final: 0.8705 (t0) REVERT: E 176 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8782 (mm-30) REVERT: Z 35 MET cc_start: 0.9104 (mmm) cc_final: 0.8872 (mmm) outliers start: 40 outliers final: 26 residues processed: 311 average time/residue: 0.0770 time to fit residues: 34.1120 Evaluate side-chains 312 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 283 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain Y residue 23 PHE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Z residue 19 ASN Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 25 ASP Chi-restraints excluded: chain Z residue 34 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 HIS ** F 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.057082 restraints weight = 23721.756| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.42 r_work: 0.2742 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9203 Z= 0.163 Angle : 0.618 9.176 12462 Z= 0.315 Chirality : 0.039 0.220 1478 Planarity : 0.003 0.022 1600 Dihedral : 3.406 16.138 1266 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.95 % Allowed : 23.29 % Favored : 72.76 % 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 aren not related in a simple way. whole: 4.17 (0.24), residues: 1183 helix: 3.05 (0.15), residues: 1057 sheet: None (None), residues: 0 loop : -0.22 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.022 0.002 TYR B 16 PHE 0.015 0.001 PHE C 156 TRP 0.020 0.001 TRP E 13 HIS 0.012 0.001 HIS F 20 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9203) covalent geometry : angle 0.61821 (12462) hydrogen bonds : bond 0.03986 ( 847) hydrogen bonds : angle 3.51978 ( 2541) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.9127 (ttpt) cc_final: 0.8869 (ttpt) REVERT: A 85 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8718 (tm) REVERT: A 89 ASN cc_start: 0.9024 (m-40) cc_final: 0.8673 (m110) REVERT: A 105 GLU cc_start: 0.8822 (mp0) cc_final: 0.8599 (mm-30) REVERT: A 109 GLU cc_start: 0.8942 (tp30) cc_final: 0.8495 (tp30) REVERT: A 176 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8391 (mp0) REVERT: B 20 ASP cc_start: 0.8879 (t70) cc_final: 0.8639 (t70) REVERT: B 72 ASN cc_start: 0.9539 (m-40) cc_final: 0.9323 (m-40) REVERT: B 116 GLU cc_start: 0.9317 (tt0) cc_final: 0.9042 (tt0) REVERT: B 208 MET cc_start: 0.9173 (tpp) cc_final: 0.8929 (tpt) REVERT: C 86 HIS cc_start: 0.8712 (t-90) cc_final: 0.8414 (t70) REVERT: C 89 ASN cc_start: 0.9312 (m-40) cc_final: 0.8994 (m110) REVERT: C 102 ASP cc_start: 0.9214 (p0) cc_final: 0.9010 (p0) REVERT: C 176 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8777 (tt0) REVERT: C 211 ASP cc_start: 0.9399 (t0) cc_final: 0.9141 (t0) REVERT: C 223 ASP cc_start: 0.9084 (m-30) cc_final: 0.8787 (m-30) REVERT: D 58 GLU cc_start: 0.9400 (mm-30) cc_final: 0.9066 (mm-30) REVERT: D 96 GLU cc_start: 0.8825 (pt0) cc_final: 0.8597 (pt0) REVERT: D 105 GLU cc_start: 0.8719 (pm20) cc_final: 0.8298 (pm20) REVERT: D 109 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8888 (mp0) REVERT: E 108 LYS cc_start: 0.9120 (mtpt) cc_final: 0.8887 (mtpt) REVERT: E 109 GLU cc_start: 0.9054 (tp30) cc_final: 0.8670 (tp30) REVERT: E 164 THR cc_start: 0.9185 (t) cc_final: 0.8851 (p) REVERT: E 166 ASN cc_start: 0.8956 (t0) cc_final: 0.8684 (t0) REVERT: E 176 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8956 (mm-30) REVERT: Y 15 MET cc_start: 0.8205 (mmm) cc_final: 0.7408 (mtm) outliers start: 37 outliers final: 28 residues processed: 303 average time/residue: 0.0725 time to fit residues: 31.3804 Evaluate side-chains 306 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Z residue 19 ASN Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 25 ASP Chi-restraints excluded: chain Z residue 34 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 86 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.0060 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 69 ASN B 86 HIS E 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.059208 restraints weight = 23430.553| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.40 r_work: 0.2795 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9203 Z= 0.136 Angle : 0.629 10.056 12462 Z= 0.318 Chirality : 0.039 0.258 1478 Planarity : 0.003 0.024 1600 Dihedral : 3.386 16.206 1266 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 4.17 % Allowed : 22.97 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.17 (0.24), residues: 1183 helix: 3.06 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -0.30 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 54 TYR 0.010 0.001 TYR B 132 PHE 0.017 0.001 PHE Y 34 TRP 0.019 0.001 TRP D 13 HIS 0.009 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9203) covalent geometry : angle 0.62866 (12462) hydrogen bonds : bond 0.03844 ( 847) hydrogen bonds : angle 3.46963 ( 2541) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 294 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9021 (mtp) cc_final: 0.8780 (mtp) REVERT: A 52 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8838 (ttpt) REVERT: A 73 ASP cc_start: 0.9400 (OUTLIER) cc_final: 0.9094 (m-30) REVERT: A 85 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8679 (tm) REVERT: A 89 ASN cc_start: 0.9024 (m-40) cc_final: 0.8706 (m110) REVERT: A 90 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8399 (tp30) REVERT: A 109 GLU cc_start: 0.8879 (tp30) cc_final: 0.8466 (tp30) REVERT: B 20 ASP cc_start: 0.8805 (t70) cc_final: 0.8603 (t70) REVERT: B 60 GLN cc_start: 0.9260 (mm110) cc_final: 0.9014 (mm-40) REVERT: B 72 ASN cc_start: 0.9516 (m-40) cc_final: 0.9287 (m-40) REVERT: B 109 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8755 (mp0) REVERT: B 116 GLU cc_start: 0.9290 (tt0) cc_final: 0.8992 (tt0) REVERT: B 208 MET cc_start: 0.9130 (tpp) cc_final: 0.8879 (tpt) REVERT: B 218 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9159 (mm) REVERT: C 86 HIS cc_start: 0.8670 (t-90) cc_final: 0.8355 (t70) REVERT: C 89 ASN cc_start: 0.9296 (m-40) cc_final: 0.8974 (m110) REVERT: C 176 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8755 (tt0) REVERT: C 211 ASP cc_start: 0.9331 (t0) cc_final: 0.9119 (t0) REVERT: C 223 ASP cc_start: 0.9114 (m-30) cc_final: 0.8806 (m-30) REVERT: D 47 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8669 (tm-30) REVERT: D 93 ASN cc_start: 0.9279 (t0) cc_final: 0.8998 (t0) REVERT: D 109 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8875 (mp0) REVERT: D 154 ASN cc_start: 0.9141 (m-40) cc_final: 0.8922 (m110) REVERT: E 108 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8881 (mtpt) REVERT: E 109 GLU cc_start: 0.9026 (tp30) cc_final: 0.8575 (tp30) REVERT: E 166 ASN cc_start: 0.8940 (t0) cc_final: 0.8700 (t0) REVERT: E 229 SER cc_start: 0.9109 (t) cc_final: 0.8892 (p) REVERT: Y 15 MET cc_start: 0.8161 (mmm) cc_final: 0.7409 (mtm) outliers start: 39 outliers final: 25 residues processed: 314 average time/residue: 0.0747 time to fit residues: 33.7036 Evaluate side-chains 308 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 277 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Z residue 19 ASN Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 25 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.057181 restraints weight = 23659.498| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.41 r_work: 0.2744 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9203 Z= 0.191 Angle : 0.691 11.300 12462 Z= 0.349 Chirality : 0.041 0.327 1478 Planarity : 0.003 0.027 1600 Dihedral : 3.406 15.505 1266 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.85 % Allowed : 24.79 % Favored : 71.37 % 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 aren not related in a simple way. whole: 4.14 (0.24), residues: 1183 helix: 3.02 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -0.20 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 118 TYR 0.026 0.002 TYR E 16 PHE 0.015 0.001 PHE Y 34 TRP 0.029 0.002 TRP B 13 HIS 0.017 0.002 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9203) covalent geometry : angle 0.69082 (12462) hydrogen bonds : bond 0.04015 ( 847) hydrogen bonds : angle 3.58317 ( 2541) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 281 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.9114 (ttpt) cc_final: 0.8875 (ttpt) REVERT: A 85 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8727 (tm) REVERT: A 89 ASN cc_start: 0.9043 (m-40) cc_final: 0.8680 (m-40) REVERT: A 105 GLU cc_start: 0.8856 (mp0) cc_final: 0.8620 (mm-30) REVERT: A 109 GLU cc_start: 0.8942 (tp30) cc_final: 0.8496 (tp30) REVERT: B 20 ASP cc_start: 0.8846 (t70) cc_final: 0.8618 (t70) REVERT: B 72 ASN cc_start: 0.9517 (m-40) cc_final: 0.9301 (m-40) REVERT: B 105 GLU cc_start: 0.8894 (mp0) cc_final: 0.8495 (tp30) REVERT: B 109 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8729 (mp0) REVERT: B 116 GLU cc_start: 0.9270 (tt0) cc_final: 0.8961 (tt0) REVERT: B 208 MET cc_start: 0.9176 (tpp) cc_final: 0.8910 (tpt) REVERT: B 218 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9177 (mm) REVERT: B 223 ASP cc_start: 0.9375 (t0) cc_final: 0.9061 (t0) REVERT: B 227 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8677 (mt-10) REVERT: C 86 HIS cc_start: 0.8686 (t-90) cc_final: 0.8365 (t70) REVERT: C 89 ASN cc_start: 0.9319 (m-40) cc_final: 0.8997 (m110) REVERT: C 176 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8764 (tt0) REVERT: C 211 ASP cc_start: 0.9378 (t0) cc_final: 0.9138 (t0) REVERT: C 223 ASP cc_start: 0.9137 (m-30) cc_final: 0.8840 (m-30) REVERT: D 93 ASN cc_start: 0.9289 (t0) cc_final: 0.9006 (t0) REVERT: D 154 ASN cc_start: 0.9144 (m-40) cc_final: 0.8927 (m110) REVERT: E 108 LYS cc_start: 0.9133 (mtpt) cc_final: 0.8892 (mtpt) REVERT: E 109 GLU cc_start: 0.9057 (tp30) cc_final: 0.8640 (tp30) REVERT: E 166 ASN cc_start: 0.9023 (t0) cc_final: 0.8694 (t0) REVERT: E 176 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9070 (mm-30) REVERT: Y 15 MET cc_start: 0.8218 (mmm) cc_final: 0.7472 (mtm) outliers start: 36 outliers final: 29 residues processed: 301 average time/residue: 0.0766 time to fit residues: 33.0752 Evaluate side-chains 308 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 276 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 25 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 0.0670 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.058993 restraints weight = 23556.791| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.43 r_work: 0.2791 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9203 Z= 0.153 Angle : 0.700 11.697 12462 Z= 0.352 Chirality : 0.041 0.341 1478 Planarity : 0.003 0.024 1600 Dihedral : 3.449 16.209 1266 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.53 % Allowed : 26.07 % Favored : 70.41 % 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 aren not related in a simple way. whole: 4.12 (0.24), residues: 1183 helix: 3.02 (0.15), residues: 1058 sheet: None (None), residues: 0 loop : -0.29 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 118 TYR 0.031 0.001 TYR E 16 PHE 0.014 0.001 PHE C 156 TRP 0.026 0.002 TRP B 13 HIS 0.017 0.002 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9203) covalent geometry : angle 0.69968 (12462) hydrogen bonds : bond 0.03938 ( 847) hydrogen bonds : angle 3.58939 ( 2541) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 290 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 18 HIS cc_start: 0.8985 (t-90) cc_final: 0.7836 (t70) REVERT: A 52 LYS cc_start: 0.9119 (ttpt) cc_final: 0.8882 (ttpt) REVERT: A 73 ASP cc_start: 0.9409 (OUTLIER) cc_final: 0.9113 (m-30) REVERT: A 85 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8743 (tm) REVERT: A 89 ASN cc_start: 0.9054 (m-40) cc_final: 0.8732 (m110) REVERT: A 109 GLU cc_start: 0.8883 (tp30) cc_final: 0.8437 (tp30) REVERT: B 20 ASP cc_start: 0.8813 (t70) cc_final: 0.8605 (t0) REVERT: B 47 GLU cc_start: 0.9135 (tp30) cc_final: 0.8733 (tm-30) REVERT: B 72 ASN cc_start: 0.9507 (m-40) cc_final: 0.9277 (m-40) REVERT: B 89 ASN cc_start: 0.9152 (m-40) cc_final: 0.8724 (m110) REVERT: B 105 GLU cc_start: 0.8912 (mp0) cc_final: 0.8702 (mp0) REVERT: B 109 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8864 (mp0) REVERT: B 116 GLU cc_start: 0.9241 (tt0) cc_final: 0.8914 (tt0) REVERT: B 208 MET cc_start: 0.9132 (tpp) cc_final: 0.8873 (tpt) REVERT: B 218 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9189 (mm) REVERT: B 223 ASP cc_start: 0.9363 (t0) cc_final: 0.9039 (t0) REVERT: B 227 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8685 (mt-10) REVERT: C 86 HIS cc_start: 0.8680 (t-90) cc_final: 0.8366 (t70) REVERT: C 176 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8756 (tt0) REVERT: C 211 ASP cc_start: 0.9328 (t0) cc_final: 0.9113 (t0) REVERT: C 223 ASP cc_start: 0.9112 (m-30) cc_final: 0.8812 (m-30) REVERT: D 93 ASN cc_start: 0.9255 (t0) cc_final: 0.9024 (t0) REVERT: D 154 ASN cc_start: 0.9165 (m-40) cc_final: 0.8941 (m110) REVERT: E 108 LYS cc_start: 0.9144 (mtpt) cc_final: 0.8910 (mtpt) REVERT: E 109 GLU cc_start: 0.9023 (tp30) cc_final: 0.8591 (tp30) REVERT: E 166 ASN cc_start: 0.9036 (t0) cc_final: 0.8713 (t0) REVERT: E 229 SER cc_start: 0.9115 (t) cc_final: 0.8912 (p) REVERT: Y 15 MET cc_start: 0.8212 (mmm) cc_final: 0.7515 (mtm) outliers start: 33 outliers final: 24 residues processed: 307 average time/residue: 0.0838 time to fit residues: 36.5104 Evaluate side-chains 310 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Z residue 21 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 112 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN ** F 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.059204 restraints weight = 23226.424| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.39 r_work: 0.2790 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9203 Z= 0.163 Angle : 0.726 11.560 12462 Z= 0.362 Chirality : 0.041 0.350 1478 Planarity : 0.003 0.021 1600 Dihedral : 3.440 18.296 1266 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.31 % Allowed : 25.85 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.06 (0.24), residues: 1183 helix: 3.00 (0.15), residues: 1055 sheet: None (None), residues: 0 loop : -0.41 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 118 TYR 0.030 0.002 TYR E 16 PHE 0.017 0.001 PHE Z 34 TRP 0.026 0.002 TRP B 13 HIS 0.016 0.002 HIS F 20 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9203) covalent geometry : angle 0.72634 (12462) hydrogen bonds : bond 0.03959 ( 847) hydrogen bonds : angle 3.59314 ( 2541) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1844.45 seconds wall clock time: 32 minutes 25.11 seconds (1945.11 seconds total)