Starting phenix.real_space_refine on Wed Sep 17 21:21:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jca_6441/09_2025/3jca_6441.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jca_6441/09_2025/3jca_6441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3jca_6441/09_2025/3jca_6441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jca_6441/09_2025/3jca_6441.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jca_6441/09_2025/3jca_6441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jca_6441/09_2025/3jca_6441.map" } resolution = 4.8 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= 0.002 sd= 0.044 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 78 5.49 5 S 44 5.16 5 C 7086 2.51 5 N 2076 2.21 5 O 2178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 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: 11466 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2096 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 243} Chain breaks: 1 Chain: "B" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2031 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 236} Chain breaks: 1 Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 393 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "D" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 393 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "E" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2096 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 243} Chain breaks: 1 Chain: "F" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2031 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 236} Chain breaks: 1 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 393 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "H" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 393 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 43} Chain: "I" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "K" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "L" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 299 SG CYS A 37 50.219 31.097 35.214 1.00117.64 S ATOM 320 SG CYS A 40 50.724 33.076 35.605 1.00129.65 S ATOM 2395 SG CYS B 37 120.732 24.422 25.373 1.00177.75 S ATOM 2416 SG CYS B 40 121.081 26.218 26.600 1.00174.63 S ATOM 5212 SG CYS E 37 91.196 65.853 35.151 1.00117.34 S ATOM 5233 SG CYS E 40 90.593 63.888 35.391 1.00131.03 S ATOM 7308 SG CYS F 37 20.729 72.530 25.394 1.00178.00 S ATOM 7329 SG CYS F 40 20.380 70.736 26.617 1.00174.87 S Time building chain proxies: 3.07, per 1000 atoms: 0.27 Number of scatterers: 11466 At special positions: 0 Unit cell: (142.79, 98.25, 94.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 44 16.00 P 78 15.00 O 2178 8.00 N 2076 7.00 C 7086 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: 1.04 Conformation dependent library (CDL) restraints added in 418.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 13 " pdb="ZN ZN A 500 " - pdb=" NE2 HIS A 9 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 37 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 9 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 13 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" ND1 HIS E 13 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 9 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 37 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 40 " pdb=" ZN F 500 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 40 " pdb="ZN ZN F 500 " - pdb=" SG CYS F 37 " pdb="ZN ZN F 500 " - pdb=" NE2 HIS F 9 " pdb="ZN ZN F 500 " - pdb=" ND1 HIS F 13 " Number of angles added : 6 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 39.2% alpha, 21.0% beta 36 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 69 through 76 removed outlier: 7.147A pdb=" N LYS A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 154 through 174 Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 202 through 209 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 15 through 24 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 150 through 171 Processing helix chain 'B' and resid 172 through 175 removed outlier: 4.134A pdb=" N GLY B 175 " --> pdb=" O GLN B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 15 through 24 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 69 through 76 removed outlier: 7.143A pdb=" N LYS E 74 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 129 through 140 Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 154 through 174 Processing helix chain 'E' and resid 179 through 194 Processing helix chain 'E' and resid 202 through 209 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 15 through 24 Processing helix chain 'F' and resid 26 through 36 Processing helix chain 'F' and resid 98 through 113 Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 129 through 139 Processing helix chain 'F' and resid 150 through 171 Processing helix chain 'F' and resid 172 through 175 removed outlier: 4.085A pdb=" N GLY F 175 " --> pdb=" O GLN F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 179 through 194 Processing helix chain 'F' and resid 202 through 209 Processing sheet with id=A, first strand: chain 'A' and resid 88 through 94 removed outlier: 3.547A pdb=" N TYR A 77 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP A 62 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 254 through 257 removed outlier: 5.629A pdb=" N VAL A 219 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'B' and resid 89 through 94 removed outlier: 6.545A pdb=" N TRP B 62 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE B 119 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 254 through 257 removed outlier: 5.600A pdb=" N VAL B 219 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N MET B 218 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'C' and resid 254 through 257 removed outlier: 5.370A pdb=" N VAL C 219 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'D' and resid 254 through 257 removed outlier: 6.598A pdb=" N TYR D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA D 238 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS D 244 " --> pdb=" O ILE D 236 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY D 231 " --> pdb=" O TRP D 221 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TRP D 221 " --> pdb=" O GLY D 231 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'E' and resid 88 through 94 removed outlier: 3.543A pdb=" N TYR E 77 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'E' and resid 254 through 257 removed outlier: 5.646A pdb=" N VAL E 219 " --> pdb=" O PRO E 232 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'F' and resid 89 through 94 removed outlier: 6.548A pdb=" N TRP F 62 " --> pdb=" O LYS F 120 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE F 119 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'F' and resid 254 through 257 removed outlier: 5.595A pdb=" N VAL F 219 " --> pdb=" O PRO F 232 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N MET F 218 " --> pdb=" O PHE F 264 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'G' and resid 254 through 257 removed outlier: 5.364A pdb=" N VAL G 219 " --> pdb=" O PRO G 232 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'H' and resid 254 through 257 removed outlier: 6.606A pdb=" N TYR H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA H 238 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS H 244 " --> pdb=" O ILE H 236 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY H 231 " --> pdb=" O TRP H 221 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TRP H 221 " --> pdb=" O GLY H 231 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2604 1.33 - 1.45: 3657 1.45 - 1.58: 5483 1.58 - 1.70: 154 1.70 - 1.82: 72 Bond restraints: 11970 Sorted by residual: bond pdb=" CA ASP G 223 " pdb=" C ASP G 223 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.30e-02 5.92e+03 1.33e+01 bond pdb=" CA ASP C 223 " pdb=" C ASP C 223 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.29e-02 6.01e+03 1.29e+01 bond pdb=" CA TRP A 208 " pdb=" CB TRP A 208 " ideal model delta sigma weight residual 1.531 1.477 0.054 1.51e-02 4.39e+03 1.28e+01 bond pdb=" CA ARG A 27 " pdb=" C ARG A 27 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.30e-02 5.92e+03 1.09e+01 bond pdb=" CA SER B 86 " pdb=" CB SER B 86 " ideal model delta sigma weight residual 1.532 1.478 0.054 1.65e-02 3.67e+03 1.08e+01 ... (remaining 11965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 15202 2.50 - 5.00: 1210 5.00 - 7.51: 174 7.51 - 10.01: 34 10.01 - 12.51: 4 Bond angle restraints: 16624 Sorted by residual: angle pdb=" C PHE E 246 " pdb=" N PRO E 247 " pdb=" CA PRO E 247 " ideal model delta sigma weight residual 119.78 130.02 -10.24 1.03e+00 9.43e-01 9.88e+01 angle pdb=" C PHE A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta sigma weight residual 119.78 129.93 -10.15 1.03e+00 9.43e-01 9.71e+01 angle pdb=" C PHE F 246 " pdb=" N PRO F 247 " pdb=" CA PRO F 247 " ideal model delta sigma weight residual 119.78 129.04 -9.26 1.03e+00 9.43e-01 8.09e+01 angle pdb=" C PHE B 246 " pdb=" N PRO B 247 " pdb=" CA PRO B 247 " ideal model delta sigma weight residual 119.78 128.99 -9.21 1.03e+00 9.43e-01 8.00e+01 angle pdb=" C LYS E 216 " pdb=" N PRO E 217 " pdb=" CA PRO E 217 " ideal model delta sigma weight residual 120.31 128.93 -8.62 9.80e-01 1.04e+00 7.74e+01 ... (remaining 16619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.88: 6304 31.88 - 63.77: 492 63.77 - 95.65: 18 95.65 - 127.54: 0 127.54 - 159.42: 2 Dihedral angle restraints: 6816 sinusoidal: 3254 harmonic: 3562 Sorted by residual: dihedral pdb=" C4' DA K 1 " pdb=" C3' DA K 1 " pdb=" O3' DA K 1 " pdb=" P DA K 2 " ideal model delta sinusoidal sigma weight residual 220.00 60.58 159.42 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' DA I 1 " pdb=" C3' DA I 1 " pdb=" O3' DA I 1 " pdb=" P DA I 2 " ideal model delta sinusoidal sigma weight residual 220.00 64.50 155.50 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C HIS A 13 " pdb=" N HIS A 13 " pdb=" CA HIS A 13 " pdb=" CB HIS A 13 " ideal model delta harmonic sigma weight residual -122.60 -131.24 8.64 0 2.50e+00 1.60e-01 1.19e+01 ... (remaining 6813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1284 0.073 - 0.147: 468 0.147 - 0.220: 36 0.220 - 0.293: 1 0.293 - 0.367: 1 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CA HIS A 13 " pdb=" N HIS A 13 " pdb=" C HIS A 13 " pdb=" CB HIS A 13 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA TRP E 208 " pdb=" N TRP E 208 " pdb=" C TRP E 208 " pdb=" CB TRP E 208 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA TRP A 208 " pdb=" N TRP A 208 " pdb=" C TRP A 208 " pdb=" CB TRP A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1787 not shown) Planarity restraints: 1856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 40 " -0.101 5.00e-02 4.00e+02 1.54e-01 3.82e+01 pdb=" N PRO E 41 " 0.267 5.00e-02 4.00e+02 pdb=" CA PRO E 41 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO E 41 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 40 " 0.091 5.00e-02 4.00e+02 1.36e-01 2.94e+01 pdb=" N PRO A 41 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 265 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C THR A 265 " -0.063 2.00e-02 2.50e+03 pdb=" O THR A 265 " 0.023 2.00e-02 2.50e+03 pdb=" OXT THR A 265 " 0.022 2.00e-02 2.50e+03 ... (remaining 1853 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 4253 2.88 - 3.38: 11041 3.38 - 3.89: 22227 3.89 - 4.39: 26011 4.39 - 4.90: 38001 Nonbonded interactions: 101533 Sorted by model distance: nonbonded pdb=" N GLU B 71 " pdb=" OE1 GLU B 71 " model vdw 2.370 3.120 nonbonded pdb=" N GLU F 71 " pdb=" OE1 GLU F 71 " model vdw 2.373 3.120 nonbonded pdb=" O5' DA K 2 " pdb=" O4' DA K 2 " model vdw 2.459 2.432 nonbonded pdb=" O PHE H 264 " pdb=" OG1 THR H 265 " model vdw 2.479 3.040 nonbonded pdb=" O PHE D 264 " pdb=" OG1 THR D 265 " model vdw 2.481 3.040 ... (remaining 101528 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 41 or resid 54 through 500)) selection = chain 'B' selection = (chain 'E' and (resid 1 through 41 or resid 54 through 500)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.500 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 : 0.017 0.740 11986 Z= 0.809 Angle : 1.807 68.485 16630 Z= 1.060 Chirality : 0.067 0.367 1790 Planarity : 0.011 0.154 1856 Dihedral : 18.843 159.419 4504 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.87 (0.21), residues: 1202 helix: -0.84 (0.21), residues: 440 sheet: 0.23 (0.42), residues: 146 loop : -1.93 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 59 TYR 0.040 0.006 TYR E 177 PHE 0.021 0.005 PHE A 110 TRP 0.040 0.009 TRP A 221 HIS 0.008 0.002 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.01203 (11970) covalent geometry : angle 1.49053 (16624) hydrogen bonds : bond 0.14423 ( 556) hydrogen bonds : angle 8.43256 ( 1484) metal coordination : bond 0.33731 ( 16) metal coordination : angle 53.84415 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.420 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9405 (mt) cc_final: 0.9054 (tt) REVERT: A 71 GLU cc_start: 0.7547 (tt0) cc_final: 0.6995 (tt0) REVERT: A 79 HIS cc_start: 0.8690 (m-70) cc_final: 0.8034 (m170) REVERT: A 90 PHE cc_start: 0.8938 (t80) cc_final: 0.8105 (t80) REVERT: A 105 HIS cc_start: 0.8914 (t70) cc_final: 0.7266 (t70) REVERT: A 118 LYS cc_start: 0.8574 (ptpt) cc_final: 0.8072 (tttp) REVERT: A 119 ILE cc_start: 0.8954 (tt) cc_final: 0.8661 (pt) REVERT: A 260 PHE cc_start: 0.8768 (m-80) cc_final: 0.8330 (m-10) REVERT: B 6 GLN cc_start: 0.8911 (mt0) cc_final: 0.8443 (tm-30) REVERT: B 25 ILE cc_start: 0.7929 (mt) cc_final: 0.7716 (mt) REVERT: B 168 LEU cc_start: 0.9302 (mt) cc_final: 0.9016 (mt) REVERT: B 169 ASN cc_start: 0.8805 (m-40) cc_final: 0.7777 (t0) REVERT: B 181 HIS cc_start: 0.8320 (m170) cc_final: 0.8102 (m170) REVERT: B 195 ASN cc_start: 0.8332 (m-40) cc_final: 0.8053 (t0) REVERT: B 261 ILE cc_start: 0.8754 (mm) cc_final: 0.8516 (pt) REVERT: C 242 TYR cc_start: 0.7899 (m-80) cc_final: 0.7256 (m-10) REVERT: C 255 TRP cc_start: 0.7736 (m100) cc_final: 0.7278 (m100) REVERT: E 19 LEU cc_start: 0.9381 (mt) cc_final: 0.9066 (tt) REVERT: E 39 ASN cc_start: 0.8959 (m-40) cc_final: 0.8743 (m110) REVERT: E 71 GLU cc_start: 0.7544 (tt0) cc_final: 0.7123 (tt0) REVERT: E 79 HIS cc_start: 0.8696 (m-70) cc_final: 0.8142 (m170) REVERT: E 94 ARG cc_start: 0.8790 (mmm160) cc_final: 0.8176 (mmt180) REVERT: E 105 HIS cc_start: 0.8941 (t70) cc_final: 0.7745 (t70) REVERT: E 119 ILE cc_start: 0.8895 (tt) cc_final: 0.8399 (pt) REVERT: E 144 VAL cc_start: 0.6543 (t) cc_final: 0.6147 (t) REVERT: E 220 MET cc_start: 0.8440 (mmm) cc_final: 0.8013 (mmm) REVERT: F 6 GLN cc_start: 0.8947 (mt0) cc_final: 0.8457 (tm-30) REVERT: F 168 LEU cc_start: 0.9313 (mt) cc_final: 0.9035 (mt) REVERT: F 169 ASN cc_start: 0.8779 (m-40) cc_final: 0.7769 (t0) REVERT: F 181 HIS cc_start: 0.8319 (m170) cc_final: 0.7942 (m170) REVERT: F 261 ILE cc_start: 0.8549 (mm) cc_final: 0.8243 (tp) REVERT: G 224 LEU cc_start: 0.8655 (mt) cc_final: 0.8319 (mp) REVERT: G 228 SER cc_start: 0.8165 (t) cc_final: 0.7925 (p) REVERT: G 233 ASP cc_start: 0.8046 (t0) cc_final: 0.7345 (t0) REVERT: G 242 TYR cc_start: 0.8053 (m-80) cc_final: 0.7399 (m-80) REVERT: G 255 TRP cc_start: 0.7571 (m100) cc_final: 0.6958 (m100) REVERT: H 242 TYR cc_start: 0.8028 (p90) cc_final: 0.7793 (p90) REVERT: H 258 ASP cc_start: 0.9335 (p0) cc_final: 0.8873 (p0) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.1238 time to fit residues: 69.1542 Evaluate side-chains 227 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN E 167 GLN F 192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.074348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.061823 restraints weight = 57974.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.063867 restraints weight = 33406.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.065271 restraints weight = 22083.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.066248 restraints weight = 16151.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.066858 restraints weight = 12819.688| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11986 Z= 0.176 Angle : 0.663 8.626 16630 Z= 0.368 Chirality : 0.044 0.184 1790 Planarity : 0.006 0.069 1856 Dihedral : 23.717 149.959 2160 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.60 (0.24), residues: 1202 helix: 0.32 (0.24), residues: 422 sheet: 0.29 (0.44), residues: 144 loop : -1.05 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 130 TYR 0.016 0.002 TYR A 77 PHE 0.021 0.002 PHE E 110 TRP 0.015 0.002 TRP F 208 HIS 0.008 0.002 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00369 (11970) covalent geometry : angle 0.65488 (16624) hydrogen bonds : bond 0.05209 ( 556) hydrogen bonds : angle 6.70031 ( 1484) metal coordination : bond 0.02513 ( 16) metal coordination : angle 5.59184 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.661 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9384 (mt) cc_final: 0.9076 (tt) REVERT: A 90 PHE cc_start: 0.8584 (t80) cc_final: 0.7413 (t80) REVERT: A 105 HIS cc_start: 0.8103 (t70) cc_final: 0.7714 (t70) REVERT: A 113 MET cc_start: 0.8972 (mtp) cc_final: 0.8585 (mtp) REVERT: A 118 LYS cc_start: 0.8201 (ptpt) cc_final: 0.7642 (tttp) REVERT: A 119 ILE cc_start: 0.8863 (tt) cc_final: 0.8508 (tt) REVERT: A 144 VAL cc_start: 0.6534 (t) cc_final: 0.6195 (t) REVERT: A 145 THR cc_start: 0.6763 (p) cc_final: 0.6469 (t) REVERT: A 150 ASN cc_start: 0.8421 (t0) cc_final: 0.8169 (t0) REVERT: A 190 VAL cc_start: 0.9407 (t) cc_final: 0.9164 (t) REVERT: A 220 MET cc_start: 0.8593 (tpp) cc_final: 0.8271 (tpp) REVERT: A 260 PHE cc_start: 0.8937 (m-80) cc_final: 0.8480 (m-80) REVERT: B 6 GLN cc_start: 0.8556 (mt0) cc_final: 0.8345 (tm-30) REVERT: B 97 GLU cc_start: 0.8241 (pm20) cc_final: 0.7811 (mt-10) REVERT: B 101 ASP cc_start: 0.7663 (m-30) cc_final: 0.7418 (m-30) REVERT: B 141 ILE cc_start: 0.9179 (mt) cc_final: 0.8893 (mm) REVERT: B 168 LEU cc_start: 0.9202 (mt) cc_final: 0.8930 (mt) REVERT: B 169 ASN cc_start: 0.8549 (m-40) cc_final: 0.8152 (t0) REVERT: B 173 LYS cc_start: 0.6966 (mmtt) cc_final: 0.6714 (ptmt) REVERT: E 19 LEU cc_start: 0.9291 (mt) cc_final: 0.9020 (tt) REVERT: E 25 ILE cc_start: 0.8827 (pt) cc_final: 0.8364 (pt) REVERT: E 29 GLN cc_start: 0.9134 (mt0) cc_final: 0.8481 (mm-40) REVERT: E 32 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8589 (mm-30) REVERT: E 39 ASN cc_start: 0.8876 (m-40) cc_final: 0.8502 (m110) REVERT: E 90 PHE cc_start: 0.8571 (t80) cc_final: 0.7454 (t80) REVERT: E 105 HIS cc_start: 0.8113 (t70) cc_final: 0.7435 (t70) REVERT: E 106 LEU cc_start: 0.9216 (mt) cc_final: 0.8872 (mt) REVERT: E 110 PHE cc_start: 0.8018 (m-80) cc_final: 0.7641 (m-80) REVERT: E 113 MET cc_start: 0.8916 (mtp) cc_final: 0.8519 (mtp) REVERT: E 134 GLU cc_start: 0.8879 (tt0) cc_final: 0.8655 (tm-30) REVERT: E 135 PHE cc_start: 0.8375 (m-10) cc_final: 0.8005 (m-80) REVERT: E 220 MET cc_start: 0.8723 (mmm) cc_final: 0.7823 (mmm) REVERT: E 221 TRP cc_start: 0.6876 (t60) cc_final: 0.6521 (t60) REVERT: E 260 PHE cc_start: 0.8907 (m-80) cc_final: 0.8496 (m-80) REVERT: F 6 GLN cc_start: 0.8670 (mt0) cc_final: 0.8391 (tm-30) REVERT: F 141 ILE cc_start: 0.9105 (mt) cc_final: 0.8818 (mm) REVERT: F 168 LEU cc_start: 0.9191 (mt) cc_final: 0.8867 (mt) REVERT: F 169 ASN cc_start: 0.8537 (m-40) cc_final: 0.7737 (t0) REVERT: F 218 MET cc_start: 0.7136 (mpp) cc_final: 0.6926 (mpp) REVERT: G 224 LEU cc_start: 0.8174 (mt) cc_final: 0.7811 (mt) REVERT: G 228 SER cc_start: 0.8075 (t) cc_final: 0.7683 (p) REVERT: G 242 TYR cc_start: 0.7786 (m-80) cc_final: 0.7516 (m-80) REVERT: G 255 TRP cc_start: 0.7863 (m100) cc_final: 0.7253 (m100) REVERT: G 256 VAL cc_start: 0.9321 (t) cc_final: 0.9088 (p) REVERT: H 242 TYR cc_start: 0.7030 (p90) cc_final: 0.6659 (p90) REVERT: H 258 ASP cc_start: 0.9271 (p0) cc_final: 0.8787 (p0) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.0934 time to fit residues: 43.3284 Evaluate side-chains 197 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 48 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN A 167 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN B 201 HIS ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN F 12 HIS F 108 GLN F 192 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.072108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.059946 restraints weight = 60813.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.061851 restraints weight = 35507.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063193 restraints weight = 23716.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.064114 restraints weight = 17438.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.064783 restraints weight = 13869.652| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11986 Z= 0.193 Angle : 0.651 7.077 16630 Z= 0.360 Chirality : 0.043 0.151 1790 Planarity : 0.006 0.056 1856 Dihedral : 23.468 147.507 2160 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.24 (0.24), residues: 1202 helix: 0.64 (0.24), residues: 422 sheet: -0.09 (0.41), residues: 158 loop : -0.69 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 94 TYR 0.026 0.002 TYR B 112 PHE 0.035 0.002 PHE E 72 TRP 0.027 0.002 TRP F 208 HIS 0.006 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00407 (11970) covalent geometry : angle 0.64573 (16624) hydrogen bonds : bond 0.05233 ( 556) hydrogen bonds : angle 6.37648 ( 1484) metal coordination : bond 0.00733 ( 16) metal coordination : angle 4.45367 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.415 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9439 (mt) cc_final: 0.9201 (tp) REVERT: A 29 GLN cc_start: 0.8787 (pt0) cc_final: 0.8585 (pt0) REVERT: A 79 HIS cc_start: 0.8062 (m170) cc_final: 0.7749 (m170) REVERT: A 90 PHE cc_start: 0.8720 (t80) cc_final: 0.7413 (t80) REVERT: A 105 HIS cc_start: 0.8148 (t70) cc_final: 0.7863 (t70) REVERT: A 113 MET cc_start: 0.8989 (mtp) cc_final: 0.8610 (mtp) REVERT: A 220 MET cc_start: 0.8941 (tpp) cc_final: 0.8026 (mmm) REVERT: B 97 GLU cc_start: 0.8360 (pm20) cc_final: 0.7835 (mm-30) REVERT: B 141 ILE cc_start: 0.9081 (mt) cc_final: 0.8784 (mm) REVERT: B 168 LEU cc_start: 0.9229 (mt) cc_final: 0.8954 (mt) REVERT: B 169 ASN cc_start: 0.8705 (m-40) cc_final: 0.8073 (t0) REVERT: B 189 PHE cc_start: 0.8938 (t80) cc_final: 0.8693 (t80) REVERT: C 224 LEU cc_start: 0.9011 (mp) cc_final: 0.7785 (mp) REVERT: C 256 VAL cc_start: 0.9374 (t) cc_final: 0.9005 (p) REVERT: E 6 GLN cc_start: 0.9037 (mt0) cc_final: 0.8601 (mm110) REVERT: E 19 LEU cc_start: 0.9338 (mt) cc_final: 0.9113 (tt) REVERT: E 25 ILE cc_start: 0.8873 (pt) cc_final: 0.8383 (pt) REVERT: E 29 GLN cc_start: 0.9138 (mt0) cc_final: 0.8632 (mm-40) REVERT: E 32 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7971 (mm-30) REVERT: E 90 PHE cc_start: 0.8434 (t80) cc_final: 0.7404 (t80) REVERT: E 105 HIS cc_start: 0.8101 (t70) cc_final: 0.7696 (t-90) REVERT: E 106 LEU cc_start: 0.9223 (mt) cc_final: 0.8948 (mt) REVERT: E 110 PHE cc_start: 0.8738 (m-80) cc_final: 0.7657 (m-80) REVERT: E 113 MET cc_start: 0.8914 (mtp) cc_final: 0.8432 (mtp) REVERT: E 134 GLU cc_start: 0.8967 (tt0) cc_final: 0.8657 (tm-30) REVERT: E 135 PHE cc_start: 0.8412 (m-10) cc_final: 0.7794 (m-80) REVERT: E 190 VAL cc_start: 0.9287 (t) cc_final: 0.9012 (t) REVERT: E 220 MET cc_start: 0.8756 (mmm) cc_final: 0.8058 (mmm) REVERT: E 221 TRP cc_start: 0.7250 (t60) cc_final: 0.6673 (t60) REVERT: E 260 PHE cc_start: 0.8745 (m-80) cc_final: 0.8382 (m-10) REVERT: F 6 GLN cc_start: 0.8499 (mt0) cc_final: 0.8216 (tm-30) REVERT: F 139 TRP cc_start: 0.8842 (m-90) cc_final: 0.8343 (m-90) REVERT: F 141 ILE cc_start: 0.9039 (mt) cc_final: 0.8711 (mm) REVERT: F 168 LEU cc_start: 0.9172 (mt) cc_final: 0.8904 (mt) REVERT: F 169 ASN cc_start: 0.8598 (m-40) cc_final: 0.7770 (t0) REVERT: F 218 MET cc_start: 0.7172 (mpp) cc_final: 0.6944 (mpp) REVERT: G 224 LEU cc_start: 0.8439 (mt) cc_final: 0.8071 (mp) REVERT: G 225 LEU cc_start: 0.8866 (mt) cc_final: 0.8503 (mm) REVERT: G 256 VAL cc_start: 0.9399 (t) cc_final: 0.9030 (p) REVERT: H 234 VAL cc_start: 0.9256 (t) cc_final: 0.8957 (t) REVERT: H 242 TYR cc_start: 0.7372 (p90) cc_final: 0.7024 (p90) REVERT: H 258 ASP cc_start: 0.9301 (p0) cc_final: 0.8843 (p0) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.0926 time to fit residues: 35.7693 Evaluate side-chains 170 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 88 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 39 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 167 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 167 GLN F 79 HIS F 192 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.062223 restraints weight = 59931.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.064160 restraints weight = 35250.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.065529 restraints weight = 23610.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.066464 restraints weight = 17377.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.066993 restraints weight = 13865.173| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11986 Z= 0.142 Angle : 0.593 7.076 16630 Z= 0.328 Chirality : 0.042 0.157 1790 Planarity : 0.007 0.198 1856 Dihedral : 23.169 144.813 2160 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.04 (0.24), residues: 1202 helix: 0.80 (0.25), residues: 422 sheet: 0.29 (0.43), residues: 144 loop : -0.52 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 94 TYR 0.019 0.002 TYR B 112 PHE 0.026 0.002 PHE E 72 TRP 0.031 0.002 TRP B 208 HIS 0.005 0.001 HIS F 182 Details of bonding type rmsd covalent geometry : bond 0.00301 (11970) covalent geometry : angle 0.58924 (16624) hydrogen bonds : bond 0.04394 ( 556) hydrogen bonds : angle 6.12425 ( 1484) metal coordination : bond 0.00683 ( 16) metal coordination : angle 3.60740 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.387 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.8965 (mt0) cc_final: 0.8365 (mm110) REVERT: A 19 LEU cc_start: 0.9380 (mt) cc_final: 0.9015 (tt) REVERT: A 79 HIS cc_start: 0.7982 (m170) cc_final: 0.7699 (m170) REVERT: A 90 PHE cc_start: 0.8506 (t80) cc_final: 0.7521 (t80) REVERT: A 105 HIS cc_start: 0.7953 (t70) cc_final: 0.7577 (t70) REVERT: A 113 MET cc_start: 0.8967 (mtp) cc_final: 0.8595 (mtp) REVERT: A 196 MET cc_start: 0.8260 (mmm) cc_final: 0.8015 (mmm) REVERT: A 220 MET cc_start: 0.9072 (tpp) cc_final: 0.8106 (mmm) REVERT: B 97 GLU cc_start: 0.8179 (pm20) cc_final: 0.7883 (mm-30) REVERT: B 141 ILE cc_start: 0.8983 (mt) cc_final: 0.8701 (mm) REVERT: B 168 LEU cc_start: 0.9258 (mt) cc_final: 0.9003 (mt) REVERT: B 169 ASN cc_start: 0.8697 (m-40) cc_final: 0.8065 (t0) REVERT: B 251 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8012 (pm20) REVERT: C 224 LEU cc_start: 0.9050 (mp) cc_final: 0.7866 (mp) REVERT: C 256 VAL cc_start: 0.9335 (t) cc_final: 0.8992 (p) REVERT: E 6 GLN cc_start: 0.8999 (mt0) cc_final: 0.8583 (mm110) REVERT: E 19 LEU cc_start: 0.9312 (mt) cc_final: 0.9060 (tt) REVERT: E 25 ILE cc_start: 0.8819 (pt) cc_final: 0.8468 (pt) REVERT: E 29 GLN cc_start: 0.9101 (mt0) cc_final: 0.8632 (mm-40) REVERT: E 90 PHE cc_start: 0.8398 (t80) cc_final: 0.7643 (t80) REVERT: E 105 HIS cc_start: 0.7628 (t70) cc_final: 0.7088 (t70) REVERT: E 106 LEU cc_start: 0.9212 (mt) cc_final: 0.8824 (mt) REVERT: E 110 PHE cc_start: 0.8725 (m-80) cc_final: 0.7889 (m-80) REVERT: E 113 MET cc_start: 0.9056 (mtp) cc_final: 0.8518 (mtp) REVERT: E 134 GLU cc_start: 0.8887 (tt0) cc_final: 0.8578 (tm-30) REVERT: E 135 PHE cc_start: 0.8124 (m-10) cc_final: 0.7736 (m-80) REVERT: E 220 MET cc_start: 0.8863 (mmm) cc_final: 0.8162 (mmm) REVERT: E 221 TRP cc_start: 0.7260 (t60) cc_final: 0.6624 (t60) REVERT: E 260 PHE cc_start: 0.8677 (m-80) cc_final: 0.8332 (m-10) REVERT: F 139 TRP cc_start: 0.8709 (m-90) cc_final: 0.8099 (m-90) REVERT: F 168 LEU cc_start: 0.9222 (mt) cc_final: 0.8949 (mt) REVERT: F 169 ASN cc_start: 0.8558 (m-40) cc_final: 0.7747 (t0) REVERT: F 218 MET cc_start: 0.7518 (mpp) cc_final: 0.7282 (mpp) REVERT: G 225 LEU cc_start: 0.8827 (mt) cc_final: 0.8522 (mm) REVERT: G 256 VAL cc_start: 0.9386 (t) cc_final: 0.9108 (p) REVERT: G 258 ASP cc_start: 0.7504 (p0) cc_final: 0.7255 (m-30) REVERT: H 242 TYR cc_start: 0.7137 (p90) cc_final: 0.6910 (p90) REVERT: H 258 ASP cc_start: 0.9363 (p0) cc_final: 0.8984 (p0) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.0846 time to fit residues: 32.4947 Evaluate side-chains 169 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN B 79 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 167 GLN F 192 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.074588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062804 restraints weight = 60317.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064753 restraints weight = 35456.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.066124 restraints weight = 23643.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.066949 restraints weight = 17321.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.067687 restraints weight = 13925.456| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11986 Z= 0.132 Angle : 0.574 6.403 16630 Z= 0.316 Chirality : 0.042 0.158 1790 Planarity : 0.006 0.129 1856 Dihedral : 22.982 141.350 2160 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.23 (0.25), residues: 1202 helix: 1.00 (0.25), residues: 426 sheet: 0.49 (0.44), residues: 142 loop : -0.47 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 94 TYR 0.018 0.002 TYR E 77 PHE 0.023 0.002 PHE F 135 TRP 0.040 0.002 TRP F 208 HIS 0.006 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00282 (11970) covalent geometry : angle 0.57029 (16624) hydrogen bonds : bond 0.04017 ( 556) hydrogen bonds : angle 5.87135 ( 1484) metal coordination : bond 0.00571 ( 16) metal coordination : angle 3.25003 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.427 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.9032 (mt0) cc_final: 0.8453 (mm110) REVERT: A 19 LEU cc_start: 0.9391 (mt) cc_final: 0.8972 (tt) REVERT: A 25 ILE cc_start: 0.8447 (pt) cc_final: 0.8062 (pt) REVERT: A 32 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 77 TYR cc_start: 0.8166 (m-80) cc_final: 0.7707 (m-10) REVERT: A 79 HIS cc_start: 0.8247 (m170) cc_final: 0.7753 (m170) REVERT: A 90 PHE cc_start: 0.8532 (t80) cc_final: 0.7632 (t80) REVERT: A 113 MET cc_start: 0.9050 (mtp) cc_final: 0.8008 (mtp) REVERT: A 196 MET cc_start: 0.8591 (mmm) cc_final: 0.7596 (tpp) REVERT: A 220 MET cc_start: 0.9047 (tpp) cc_final: 0.8174 (mmm) REVERT: B 97 GLU cc_start: 0.8213 (pm20) cc_final: 0.7993 (mm-30) REVERT: B 141 ILE cc_start: 0.8894 (mt) cc_final: 0.8624 (mm) REVERT: B 156 ILE cc_start: 0.7319 (mm) cc_final: 0.6905 (mm) REVERT: B 168 LEU cc_start: 0.9295 (mt) cc_final: 0.9036 (mt) REVERT: B 169 ASN cc_start: 0.8681 (m-40) cc_final: 0.8007 (t0) REVERT: B 251 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7990 (pm20) REVERT: C 224 LEU cc_start: 0.8312 (mp) cc_final: 0.7047 (mp) REVERT: C 256 VAL cc_start: 0.9405 (t) cc_final: 0.8991 (p) REVERT: E 6 GLN cc_start: 0.9028 (mt0) cc_final: 0.8792 (mm110) REVERT: E 19 LEU cc_start: 0.9285 (mt) cc_final: 0.8967 (tt) REVERT: E 25 ILE cc_start: 0.8805 (pt) cc_final: 0.8389 (pt) REVERT: E 29 GLN cc_start: 0.9125 (mt0) cc_final: 0.8613 (mm-40) REVERT: E 32 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8343 (mm-30) REVERT: E 90 PHE cc_start: 0.8466 (t80) cc_final: 0.7703 (t80) REVERT: E 105 HIS cc_start: 0.7986 (t70) cc_final: 0.7522 (t70) REVERT: E 106 LEU cc_start: 0.9220 (mt) cc_final: 0.8848 (mt) REVERT: E 110 PHE cc_start: 0.8685 (m-80) cc_final: 0.7993 (m-80) REVERT: E 113 MET cc_start: 0.9074 (mtp) cc_final: 0.8644 (mtp) REVERT: E 134 GLU cc_start: 0.8979 (tt0) cc_final: 0.8594 (tm-30) REVERT: E 135 PHE cc_start: 0.8179 (m-10) cc_final: 0.7871 (m-80) REVERT: E 220 MET cc_start: 0.8923 (mmm) cc_final: 0.8174 (mmm) REVERT: E 221 TRP cc_start: 0.7314 (t60) cc_final: 0.6636 (t60) REVERT: E 260 PHE cc_start: 0.8742 (m-80) cc_final: 0.8389 (m-10) REVERT: F 139 TRP cc_start: 0.8649 (m-90) cc_final: 0.8143 (m-90) REVERT: F 168 LEU cc_start: 0.9266 (mt) cc_final: 0.9036 (mt) REVERT: F 169 ASN cc_start: 0.8556 (m-40) cc_final: 0.7705 (t0) REVERT: F 218 MET cc_start: 0.7525 (mpp) cc_final: 0.7324 (mpp) REVERT: G 224 LEU cc_start: 0.8394 (mp) cc_final: 0.7818 (mp) REVERT: G 225 LEU cc_start: 0.8844 (mt) cc_final: 0.8566 (mm) REVERT: H 242 TYR cc_start: 0.7281 (p90) cc_final: 0.7051 (p90) REVERT: H 258 ASP cc_start: 0.9364 (p0) cc_final: 0.8971 (p0) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.0963 time to fit residues: 35.7600 Evaluate side-chains 163 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 102 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 91 optimal weight: 0.0040 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 167 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN F 172 GLN F 192 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.073298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.061652 restraints weight = 60168.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.063551 restraints weight = 35181.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.064878 restraints weight = 23411.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.065697 restraints weight = 17134.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066388 restraints weight = 13695.656| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11986 Z= 0.145 Angle : 0.575 5.548 16630 Z= 0.319 Chirality : 0.042 0.164 1790 Planarity : 0.006 0.109 1856 Dihedral : 22.916 139.908 2160 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.10 % Allowed : 1.06 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.28 (0.25), residues: 1202 helix: 1.16 (0.26), residues: 424 sheet: 0.27 (0.43), residues: 144 loop : -0.47 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 94 TYR 0.015 0.002 TYR E 77 PHE 0.017 0.002 PHE B 189 TRP 0.037 0.002 TRP B 208 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00310 (11970) covalent geometry : angle 0.57305 (16624) hydrogen bonds : bond 0.04064 ( 556) hydrogen bonds : angle 5.85102 ( 1484) metal coordination : bond 0.00435 ( 16) metal coordination : angle 2.44010 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.374 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.9056 (mt0) cc_final: 0.8811 (mm110) REVERT: A 19 LEU cc_start: 0.9441 (mt) cc_final: 0.8806 (tp) REVERT: A 77 TYR cc_start: 0.8161 (m-80) cc_final: 0.7517 (m-10) REVERT: A 79 HIS cc_start: 0.8461 (m170) cc_final: 0.8064 (m170) REVERT: A 90 PHE cc_start: 0.8641 (t80) cc_final: 0.7796 (t80) REVERT: A 194 VAL cc_start: 0.8837 (t) cc_final: 0.6952 (t) REVERT: A 196 MET cc_start: 0.8445 (mmm) cc_final: 0.8011 (mmt) REVERT: A 220 MET cc_start: 0.9030 (tpp) cc_final: 0.8344 (mmm) REVERT: B 141 ILE cc_start: 0.8875 (mt) cc_final: 0.8607 (mm) REVERT: B 168 LEU cc_start: 0.9328 (mt) cc_final: 0.9059 (mt) REVERT: B 169 ASN cc_start: 0.8680 (m-40) cc_final: 0.7989 (t0) REVERT: B 251 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8164 (pm20) REVERT: C 224 LEU cc_start: 0.8284 (mp) cc_final: 0.7819 (mp) REVERT: C 256 VAL cc_start: 0.9424 (t) cc_final: 0.9128 (p) REVERT: E 6 GLN cc_start: 0.9095 (mt0) cc_final: 0.8862 (mm110) REVERT: E 19 LEU cc_start: 0.9435 (mt) cc_final: 0.8977 (tt) REVERT: E 25 ILE cc_start: 0.8809 (pt) cc_final: 0.8357 (pt) REVERT: E 29 GLN cc_start: 0.9137 (mt0) cc_final: 0.8663 (mm-40) REVERT: E 90 PHE cc_start: 0.8538 (t80) cc_final: 0.7765 (t80) REVERT: E 105 HIS cc_start: 0.8024 (t70) cc_final: 0.7178 (t70) REVERT: E 106 LEU cc_start: 0.9280 (mt) cc_final: 0.8904 (mt) REVERT: E 110 PHE cc_start: 0.8767 (m-80) cc_final: 0.8084 (m-80) REVERT: E 113 MET cc_start: 0.9043 (mtp) cc_final: 0.8577 (mtp) REVERT: E 134 GLU cc_start: 0.8846 (tt0) cc_final: 0.8518 (tm-30) REVERT: E 135 PHE cc_start: 0.8078 (m-10) cc_final: 0.7668 (m-80) REVERT: E 196 MET cc_start: 0.8559 (mmm) cc_final: 0.8258 (mmm) REVERT: E 220 MET cc_start: 0.8873 (mmm) cc_final: 0.8205 (mmm) REVERT: E 221 TRP cc_start: 0.7436 (t60) cc_final: 0.6691 (t60) REVERT: E 260 PHE cc_start: 0.8721 (m-80) cc_final: 0.8346 (m-10) REVERT: F 110 PHE cc_start: 0.8686 (m-10) cc_final: 0.8482 (m-10) REVERT: F 139 TRP cc_start: 0.8586 (m-90) cc_final: 0.7884 (m-90) REVERT: F 168 LEU cc_start: 0.9303 (mt) cc_final: 0.9043 (mt) REVERT: F 169 ASN cc_start: 0.8546 (m-40) cc_final: 0.7672 (t0) REVERT: G 224 LEU cc_start: 0.8313 (mp) cc_final: 0.8090 (mp) REVERT: G 225 LEU cc_start: 0.8825 (mt) cc_final: 0.8616 (mm) REVERT: G 256 VAL cc_start: 0.9330 (t) cc_final: 0.8964 (p) REVERT: H 234 VAL cc_start: 0.8992 (m) cc_final: 0.8610 (p) REVERT: H 242 TYR cc_start: 0.7325 (p90) cc_final: 0.7060 (p90) REVERT: H 258 ASP cc_start: 0.9347 (p0) cc_final: 0.8933 (p0) outliers start: 1 outliers final: 1 residues processed: 234 average time/residue: 0.0831 time to fit residues: 29.8217 Evaluate side-chains 158 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 114 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN E 207 HIS F 192 ASN F 195 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.068231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.056880 restraints weight = 62176.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.058655 restraints weight = 36043.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.059813 restraints weight = 24012.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.060772 restraints weight = 17872.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061281 restraints weight = 14134.253| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11986 Z= 0.271 Angle : 0.735 9.872 16630 Z= 0.405 Chirality : 0.045 0.210 1790 Planarity : 0.007 0.139 1856 Dihedral : 23.237 140.323 2160 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.36 (0.24), residues: 1202 helix: 0.58 (0.25), residues: 420 sheet: -0.42 (0.40), residues: 160 loop : -0.69 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 94 TYR 0.027 0.003 TYR D 242 PHE 0.025 0.003 PHE F 189 TRP 0.034 0.003 TRP F 208 HIS 0.008 0.002 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00573 (11970) covalent geometry : angle 0.72648 (16624) hydrogen bonds : bond 0.05395 ( 556) hydrogen bonds : angle 6.45746 ( 1484) metal coordination : bond 0.01782 ( 16) metal coordination : angle 5.94996 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.408 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: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.9153 (mt0) cc_final: 0.8556 (mm110) REVERT: A 72 PHE cc_start: 0.7330 (m-80) cc_final: 0.7071 (m-80) REVERT: A 79 HIS cc_start: 0.8486 (m170) cc_final: 0.8259 (m170) REVERT: A 83 ASP cc_start: 0.8896 (t0) cc_final: 0.8181 (t0) REVERT: A 90 PHE cc_start: 0.8698 (t80) cc_final: 0.7808 (t80) REVERT: A 196 MET cc_start: 0.8399 (mmm) cc_final: 0.7794 (mmm) REVERT: A 220 MET cc_start: 0.8913 (tpp) cc_final: 0.8298 (mmm) REVERT: B 141 ILE cc_start: 0.8951 (mt) cc_final: 0.8717 (mm) REVERT: B 168 LEU cc_start: 0.9345 (mt) cc_final: 0.9087 (mt) REVERT: B 169 ASN cc_start: 0.8612 (m-40) cc_final: 0.8103 (t0) REVERT: C 224 LEU cc_start: 0.8408 (mp) cc_final: 0.7878 (mp) REVERT: C 256 VAL cc_start: 0.9480 (t) cc_final: 0.9147 (p) REVERT: D 245 VAL cc_start: 0.9046 (m) cc_final: 0.8668 (p) REVERT: D 258 ASP cc_start: 0.9342 (p0) cc_final: 0.9108 (p0) REVERT: E 6 GLN cc_start: 0.9119 (mt0) cc_final: 0.8896 (mm110) REVERT: E 14 GLN cc_start: 0.7596 (tp40) cc_final: 0.7225 (tp40) REVERT: E 90 PHE cc_start: 0.8736 (t80) cc_final: 0.7684 (t80) REVERT: E 106 LEU cc_start: 0.9392 (mt) cc_final: 0.9167 (mt) REVERT: E 113 MET cc_start: 0.9122 (mtp) cc_final: 0.8726 (mtp) REVERT: E 134 GLU cc_start: 0.8941 (tt0) cc_final: 0.8612 (tm-30) REVERT: E 135 PHE cc_start: 0.8269 (m-10) cc_final: 0.7430 (m-80) REVERT: E 188 LEU cc_start: 0.9438 (mt) cc_final: 0.9215 (mt) REVERT: E 196 MET cc_start: 0.8535 (mmm) cc_final: 0.8252 (mmm) REVERT: E 220 MET cc_start: 0.8799 (mmm) cc_final: 0.8276 (mmm) REVERT: F 139 TRP cc_start: 0.8544 (m-90) cc_final: 0.7868 (m-90) REVERT: F 168 LEU cc_start: 0.9340 (mt) cc_final: 0.9073 (mt) REVERT: F 169 ASN cc_start: 0.8579 (m-40) cc_final: 0.7877 (t0) REVERT: G 224 LEU cc_start: 0.8329 (mp) cc_final: 0.7872 (mp) REVERT: G 240 ARG cc_start: 0.8452 (mtm-85) cc_final: 0.8045 (mtp180) REVERT: G 256 VAL cc_start: 0.9411 (t) cc_final: 0.9026 (p) REVERT: H 223 ASP cc_start: 0.8072 (t0) cc_final: 0.7776 (t0) REVERT: H 234 VAL cc_start: 0.9321 (m) cc_final: 0.8977 (p) REVERT: H 258 ASP cc_start: 0.9339 (p0) cc_final: 0.9017 (p0) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.0883 time to fit residues: 27.6136 Evaluate side-chains 147 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 0.0980 chunk 23 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN A 68 HIS ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.069757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.058725 restraints weight = 62011.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060454 restraints weight = 37144.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061653 restraints weight = 24909.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.062359 restraints weight = 18470.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.062951 restraints weight = 15002.538| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11986 Z= 0.193 Angle : 0.652 8.564 16630 Z= 0.358 Chirality : 0.044 0.302 1790 Planarity : 0.006 0.108 1856 Dihedral : 23.044 139.773 2160 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.52 (0.24), residues: 1202 helix: 0.55 (0.24), residues: 426 sheet: -0.59 (0.41), residues: 150 loop : -0.87 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 206 TYR 0.020 0.002 TYR E 77 PHE 0.032 0.002 PHE E 72 TRP 0.033 0.002 TRP F 208 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00410 (11970) covalent geometry : angle 0.64466 (16624) hydrogen bonds : bond 0.04520 ( 556) hydrogen bonds : angle 6.30857 ( 1484) metal coordination : bond 0.00963 ( 16) metal coordination : angle 5.03838 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.433 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: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.9249 (mt0) cc_final: 0.8680 (pt0) REVERT: A 72 PHE cc_start: 0.7367 (m-80) cc_final: 0.7057 (m-80) REVERT: A 77 TYR cc_start: 0.8175 (m-80) cc_final: 0.7827 (m-10) REVERT: A 79 HIS cc_start: 0.8441 (m170) cc_final: 0.7912 (m170) REVERT: A 83 ASP cc_start: 0.8815 (t0) cc_final: 0.7169 (p0) REVERT: A 90 PHE cc_start: 0.8744 (t80) cc_final: 0.7616 (t80) REVERT: A 196 MET cc_start: 0.8250 (mmm) cc_final: 0.7700 (mmm) REVERT: A 220 MET cc_start: 0.8895 (tpp) cc_final: 0.8306 (mmm) REVERT: A 221 TRP cc_start: 0.7855 (t60) cc_final: 0.7544 (t60) REVERT: B 168 LEU cc_start: 0.9324 (mt) cc_final: 0.9051 (mt) REVERT: B 169 ASN cc_start: 0.8607 (m-40) cc_final: 0.8113 (t0) REVERT: C 224 LEU cc_start: 0.8586 (mp) cc_final: 0.8187 (mp) REVERT: C 256 VAL cc_start: 0.9493 (t) cc_final: 0.9248 (p) REVERT: D 245 VAL cc_start: 0.9116 (m) cc_final: 0.8628 (p) REVERT: E 6 GLN cc_start: 0.9106 (mt0) cc_final: 0.8862 (mm110) REVERT: E 19 LEU cc_start: 0.9455 (mt) cc_final: 0.9219 (mt) REVERT: E 90 PHE cc_start: 0.8736 (t80) cc_final: 0.7913 (t80) REVERT: E 106 LEU cc_start: 0.9404 (mt) cc_final: 0.9049 (mt) REVERT: E 110 PHE cc_start: 0.8984 (m-80) cc_final: 0.8521 (m-80) REVERT: E 113 MET cc_start: 0.8878 (mtp) cc_final: 0.7912 (mtp) REVERT: E 134 GLU cc_start: 0.8880 (tt0) cc_final: 0.8564 (tm-30) REVERT: E 135 PHE cc_start: 0.7983 (m-10) cc_final: 0.7324 (m-80) REVERT: E 188 LEU cc_start: 0.9288 (mt) cc_final: 0.9009 (mt) REVERT: E 196 MET cc_start: 0.8701 (mmm) cc_final: 0.8083 (mmm) REVERT: E 220 MET cc_start: 0.8702 (mmm) cc_final: 0.8270 (mmm) REVERT: E 221 TRP cc_start: 0.8151 (t60) cc_final: 0.7831 (t60) REVERT: F 139 TRP cc_start: 0.8405 (m-90) cc_final: 0.7870 (m-90) REVERT: F 168 LEU cc_start: 0.9291 (mt) cc_final: 0.9041 (mt) REVERT: F 169 ASN cc_start: 0.8527 (m-40) cc_final: 0.7863 (t0) REVERT: F 196 MET cc_start: 0.6459 (mtt) cc_final: 0.6192 (mtp) REVERT: G 224 LEU cc_start: 0.8395 (mp) cc_final: 0.7980 (mp) REVERT: G 240 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8155 (mtp180) REVERT: G 256 VAL cc_start: 0.9418 (t) cc_final: 0.9046 (p) REVERT: H 234 VAL cc_start: 0.9239 (m) cc_final: 0.8847 (p) REVERT: H 258 ASP cc_start: 0.9193 (p0) cc_final: 0.8968 (p0) outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 0.0893 time to fit residues: 28.2686 Evaluate side-chains 143 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN A 52 ASN A 68 HIS ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.058473 restraints weight = 61162.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060162 restraints weight = 36607.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.061365 restraints weight = 24633.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.062206 restraints weight = 18208.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.062665 restraints weight = 14537.542| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11986 Z= 0.179 Angle : 0.641 8.190 16630 Z= 0.352 Chirality : 0.044 0.238 1790 Planarity : 0.006 0.090 1856 Dihedral : 22.948 138.116 2160 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.10 % Allowed : 0.48 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.55 (0.24), residues: 1202 helix: 0.58 (0.25), residues: 426 sheet: -0.56 (0.40), residues: 156 loop : -0.95 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 94 TYR 0.017 0.002 TYR E 77 PHE 0.031 0.002 PHE E 72 TRP 0.053 0.002 TRP B 208 HIS 0.007 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00385 (11970) covalent geometry : angle 0.63494 (16624) hydrogen bonds : bond 0.04331 ( 556) hydrogen bonds : angle 6.29215 ( 1484) metal coordination : bond 0.00814 ( 16) metal coordination : angle 4.80032 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.428 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: symmetry clash REVERT: A 6 GLN cc_start: 0.9261 (mt0) cc_final: 0.8659 (pt0) REVERT: A 15 ASN cc_start: 0.7311 (t0) cc_final: 0.7109 (t0) REVERT: A 72 PHE cc_start: 0.7355 (m-80) cc_final: 0.7114 (m-80) REVERT: A 79 HIS cc_start: 0.8422 (m170) cc_final: 0.7982 (m170) REVERT: A 83 ASP cc_start: 0.8809 (t0) cc_final: 0.7044 (p0) REVERT: A 90 PHE cc_start: 0.8703 (t80) cc_final: 0.7749 (t80) REVERT: A 106 LEU cc_start: 0.9367 (mt) cc_final: 0.9095 (mt) REVERT: A 113 MET cc_start: 0.9141 (mtm) cc_final: 0.8202 (mtp) REVERT: A 188 LEU cc_start: 0.9364 (mt) cc_final: 0.9116 (mt) REVERT: A 192 ASN cc_start: 0.8740 (m-40) cc_final: 0.8504 (m-40) REVERT: A 196 MET cc_start: 0.8419 (mmm) cc_final: 0.7835 (mmm) REVERT: A 220 MET cc_start: 0.8874 (tpp) cc_final: 0.8274 (mmm) REVERT: A 221 TRP cc_start: 0.7996 (t60) cc_final: 0.7674 (t60) REVERT: B 139 TRP cc_start: 0.8449 (m-90) cc_final: 0.8234 (m-90) REVERT: B 168 LEU cc_start: 0.9305 (mt) cc_final: 0.9044 (mt) REVERT: B 169 ASN cc_start: 0.8624 (m-40) cc_final: 0.8122 (t0) REVERT: C 224 LEU cc_start: 0.8675 (mp) cc_final: 0.8246 (mp) REVERT: C 256 VAL cc_start: 0.9491 (t) cc_final: 0.9254 (p) REVERT: D 245 VAL cc_start: 0.9185 (m) cc_final: 0.8659 (p) REVERT: E 6 GLN cc_start: 0.9126 (mt0) cc_final: 0.8908 (mm110) REVERT: E 14 GLN cc_start: 0.7285 (tp40) cc_final: 0.6889 (tp40) REVERT: E 19 LEU cc_start: 0.9491 (mt) cc_final: 0.9273 (mt) REVERT: E 56 LEU cc_start: 0.9287 (mm) cc_final: 0.8567 (tp) REVERT: E 90 PHE cc_start: 0.8727 (t80) cc_final: 0.7791 (t80) REVERT: E 106 LEU cc_start: 0.9380 (mt) cc_final: 0.9119 (mt) REVERT: E 113 MET cc_start: 0.8807 (mtp) cc_final: 0.8361 (mtp) REVERT: E 134 GLU cc_start: 0.8907 (tt0) cc_final: 0.8619 (tm-30) REVERT: E 135 PHE cc_start: 0.7851 (m-10) cc_final: 0.7181 (m-80) REVERT: E 188 LEU cc_start: 0.9300 (mt) cc_final: 0.9044 (mt) REVERT: E 196 MET cc_start: 0.8674 (mmm) cc_final: 0.8022 (mmm) REVERT: E 211 ILE cc_start: 0.7014 (mt) cc_final: 0.6766 (mt) REVERT: E 220 MET cc_start: 0.8700 (mmm) cc_final: 0.8215 (mmm) REVERT: E 221 TRP cc_start: 0.8220 (t60) cc_final: 0.7885 (t60) REVERT: F 139 TRP cc_start: 0.8422 (m-90) cc_final: 0.7791 (m-90) REVERT: F 168 LEU cc_start: 0.9287 (mt) cc_final: 0.9037 (mt) REVERT: F 169 ASN cc_start: 0.8515 (m-40) cc_final: 0.7838 (t0) REVERT: G 224 LEU cc_start: 0.8505 (mp) cc_final: 0.8095 (mp) REVERT: G 240 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8173 (mtp180) REVERT: G 256 VAL cc_start: 0.9415 (t) cc_final: 0.9020 (p) REVERT: H 234 VAL cc_start: 0.9203 (m) cc_final: 0.8884 (p) REVERT: H 237 THR cc_start: 0.5948 (t) cc_final: 0.5717 (t) REVERT: H 258 ASP cc_start: 0.9174 (p0) cc_final: 0.8920 (p0) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.0794 time to fit residues: 24.6051 Evaluate side-chains 145 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 ASN ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.067797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057063 restraints weight = 62763.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.058677 restraints weight = 37431.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.059806 restraints weight = 25365.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.060666 restraints weight = 18906.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.061119 restraints weight = 14989.973| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.7019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11986 Z= 0.243 Angle : 0.707 11.881 16630 Z= 0.386 Chirality : 0.045 0.183 1790 Planarity : 0.006 0.098 1856 Dihedral : 23.132 137.347 2160 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.96 (0.24), residues: 1202 helix: 0.29 (0.25), residues: 426 sheet: -0.83 (0.40), residues: 160 loop : -1.22 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 240 TYR 0.019 0.002 TYR E 77 PHE 0.029 0.003 PHE E 72 TRP 0.075 0.003 TRP F 208 HIS 0.008 0.002 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00521 (11970) covalent geometry : angle 0.69604 (16624) hydrogen bonds : bond 0.04909 ( 556) hydrogen bonds : angle 6.61215 ( 1484) metal coordination : bond 0.01250 ( 16) metal coordination : angle 6.55949 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.370 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: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.9261 (mt0) cc_final: 0.8754 (pt0) REVERT: A 15 ASN cc_start: 0.7711 (t0) cc_final: 0.7284 (p0) REVERT: A 56 LEU cc_start: 0.9401 (mm) cc_final: 0.8518 (tp) REVERT: A 79 HIS cc_start: 0.8285 (m170) cc_final: 0.8010 (m170) REVERT: A 83 ASP cc_start: 0.8844 (t0) cc_final: 0.7182 (p0) REVERT: A 106 LEU cc_start: 0.9437 (mt) cc_final: 0.9207 (mt) REVERT: A 113 MET cc_start: 0.9204 (mtm) cc_final: 0.8824 (mtm) REVERT: A 188 LEU cc_start: 0.9375 (mt) cc_final: 0.9170 (mt) REVERT: A 196 MET cc_start: 0.8498 (mmm) cc_final: 0.7882 (mmm) REVERT: A 220 MET cc_start: 0.8866 (tpp) cc_final: 0.8263 (mmm) REVERT: A 221 TRP cc_start: 0.8174 (t60) cc_final: 0.7810 (t60) REVERT: B 139 TRP cc_start: 0.8568 (m-90) cc_final: 0.8342 (m-90) REVERT: B 168 LEU cc_start: 0.9361 (mt) cc_final: 0.9130 (mt) REVERT: B 169 ASN cc_start: 0.8640 (m-40) cc_final: 0.8163 (t0) REVERT: C 224 LEU cc_start: 0.8669 (mp) cc_final: 0.8227 (mp) REVERT: D 245 VAL cc_start: 0.9185 (m) cc_final: 0.8571 (p) REVERT: D 258 ASP cc_start: 0.9329 (p0) cc_final: 0.9069 (p0) REVERT: E 6 GLN cc_start: 0.9157 (mt0) cc_final: 0.8940 (mm110) REVERT: E 19 LEU cc_start: 0.9546 (mt) cc_final: 0.9314 (mt) REVERT: E 83 ASP cc_start: 0.8531 (t0) cc_final: 0.7701 (t0) REVERT: E 90 PHE cc_start: 0.8804 (t80) cc_final: 0.7914 (t80) REVERT: E 106 LEU cc_start: 0.9451 (mt) cc_final: 0.9189 (mt) REVERT: E 113 MET cc_start: 0.8761 (mtp) cc_final: 0.8531 (mtp) REVERT: E 134 GLU cc_start: 0.8956 (tt0) cc_final: 0.8717 (tm-30) REVERT: E 135 PHE cc_start: 0.7966 (m-10) cc_final: 0.7272 (m-80) REVERT: E 188 LEU cc_start: 0.9295 (mt) cc_final: 0.9080 (mt) REVERT: E 220 MET cc_start: 0.8708 (mmm) cc_final: 0.8203 (mmm) REVERT: E 221 TRP cc_start: 0.8340 (t60) cc_final: 0.7438 (t60) REVERT: F 139 TRP cc_start: 0.8470 (m-90) cc_final: 0.7759 (m-90) REVERT: F 168 LEU cc_start: 0.9390 (mt) cc_final: 0.9146 (mt) REVERT: F 169 ASN cc_start: 0.8544 (m-40) cc_final: 0.7891 (t0) REVERT: F 208 TRP cc_start: 0.8175 (m100) cc_final: 0.7881 (m100) REVERT: G 224 LEU cc_start: 0.8489 (mp) cc_final: 0.8068 (mp) REVERT: G 256 VAL cc_start: 0.9378 (t) cc_final: 0.9078 (p) REVERT: H 234 VAL cc_start: 0.9284 (m) cc_final: 0.8999 (p) REVERT: H 237 THR cc_start: 0.5449 (t) cc_final: 0.5209 (t) REVERT: H 242 TYR cc_start: 0.7315 (p90) cc_final: 0.7049 (p90) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.0855 time to fit residues: 25.0476 Evaluate side-chains 144 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 86 optimal weight: 0.0070 chunk 87 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 54 optimal weight: 0.0370 chunk 36 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.9878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 ASN A 79 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS F 192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.070512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.059382 restraints weight = 61190.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.061113 restraints weight = 36311.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.062327 restraints weight = 24301.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063057 restraints weight = 17900.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.063693 restraints weight = 14385.450| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11986 Z= 0.149 Angle : 0.610 7.553 16630 Z= 0.336 Chirality : 0.043 0.151 1790 Planarity : 0.005 0.084 1856 Dihedral : 22.959 136.023 2160 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.63 (0.24), residues: 1202 helix: 0.56 (0.25), residues: 426 sheet: -0.40 (0.41), residues: 156 loop : -1.10 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 240 TYR 0.018 0.002 TYR B 112 PHE 0.028 0.002 PHE B 264 TRP 0.046 0.002 TRP B 208 HIS 0.006 0.001 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00323 (11970) covalent geometry : angle 0.60510 (16624) hydrogen bonds : bond 0.04085 ( 556) hydrogen bonds : angle 6.21542 ( 1484) metal coordination : bond 0.00765 ( 16) metal coordination : angle 3.95739 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.66 seconds wall clock time: 31 minutes 38.81 seconds (1898.81 seconds total)