Starting phenix.real_space_refine on Tue Jun 10 07:25:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jca_6441/06_2025/3jca_6441.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jca_6441/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/3jca_6441/06_2025/3jca_6441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jca_6441/06_2025/3jca_6441.map" model { file = "/net/cci-nas-00/data/ceres_data/3jca_6441/06_2025/3jca_6441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jca_6441/06_2025/3jca_6441.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.86, per 1000 atoms: 0.86 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: 4.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 4.94 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: 4.73 Time building geometry restraints manager: 5.42 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 41 or resid 54 through 265 or resid 500)) selection = chain 'B' selection = (chain 'E' and (resid 1 through 41 or resid 54 through 265 or resid 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: 272.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.170 Process input model: 42.290 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 319.690 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.040 0.009 TRP A 221 HIS 0.008 0.002 HIS B 13 PHE 0.021 0.005 PHE A 110 TYR 0.040 0.006 TYR E 177 ARG 0.005 0.001 ARG A 59 Details of bonding type rmsd hydrogen bonds : bond 0.14423 ( 556) hydrogen bonds : angle 8.43256 ( 1484) metal coordination : bond 0.33731 ( 16) metal coordination : angle 53.84415 ( 6) covalent geometry : bond 0.01203 (11970) covalent geometry : angle 1.49053 (16624) *********************** 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 : 1.369 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: 0.3737 time to fit residues: 207.7114 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 : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3468 r_free = 0.3468 target = 0.074769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.062413 restraints weight = 55940.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.064397 restraints weight = 32631.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.065805 restraints weight = 21766.368| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11986 Z= 0.171 Angle : 0.669 10.455 16630 Z= 0.369 Chirality : 0.044 0.209 1790 Planarity : 0.006 0.067 1856 Dihedral : 23.749 150.216 2160 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.35 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1202 helix: 0.33 (0.24), residues: 422 sheet: 0.31 (0.44), residues: 144 loop : -1.05 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 208 HIS 0.007 0.001 HIS F 182 PHE 0.022 0.002 PHE E 110 TYR 0.016 0.002 TYR A 77 ARG 0.006 0.001 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.05233 ( 556) hydrogen bonds : angle 6.71528 ( 1484) metal coordination : bond 0.02135 ( 16) metal coordination : angle 7.25207 ( 6) covalent geometry : bond 0.00367 (11970) covalent geometry : angle 0.65507 (16624) *********************** 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 319 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.215 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: A 19 LEU cc_start: 0.9377 (mt) cc_final: 0.9029 (tt) REVERT: A 90 PHE cc_start: 0.8558 (t80) cc_final: 0.7417 (t80) REVERT: A 105 HIS cc_start: 0.8064 (t70) cc_final: 0.7597 (t70) REVERT: A 113 MET cc_start: 0.8978 (mtp) cc_final: 0.8555 (mtp) REVERT: A 118 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7590 (tttp) REVERT: A 119 ILE cc_start: 0.8865 (tt) cc_final: 0.8624 (tt) REVERT: A 145 THR cc_start: 0.6831 (p) cc_final: 0.6546 (t) REVERT: A 150 ASN cc_start: 0.8379 (t0) cc_final: 0.8165 (t0) REVERT: A 190 VAL cc_start: 0.9403 (t) cc_final: 0.9147 (t) REVERT: A 218 MET cc_start: 0.6912 (mtp) cc_final: 0.6711 (ptm) REVERT: A 260 PHE cc_start: 0.8932 (m-80) cc_final: 0.8522 (m-80) REVERT: B 6 GLN cc_start: 0.8582 (mt0) cc_final: 0.8352 (tm-30) REVERT: B 39 ASN cc_start: 0.6038 (t0) cc_final: 0.5815 (m110) REVERT: B 97 GLU cc_start: 0.8354 (pm20) cc_final: 0.7873 (mt-10) REVERT: B 101 ASP cc_start: 0.7643 (m-30) cc_final: 0.7384 (m-30) REVERT: B 141 ILE cc_start: 0.9148 (mt) cc_final: 0.8853 (mm) REVERT: B 168 LEU cc_start: 0.9209 (mt) cc_final: 0.8941 (mt) REVERT: B 169 ASN cc_start: 0.8552 (m-40) cc_final: 0.8164 (t0) REVERT: B 173 LYS cc_start: 0.6941 (mmtt) cc_final: 0.6644 (ptmt) REVERT: E 19 LEU cc_start: 0.9291 (mt) cc_final: 0.9018 (tt) REVERT: E 25 ILE cc_start: 0.8811 (pt) cc_final: 0.8357 (pt) REVERT: E 29 GLN cc_start: 0.9129 (mt0) cc_final: 0.8473 (mm-40) REVERT: E 32 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8577 (mm-30) REVERT: E 39 ASN cc_start: 0.8878 (m-40) cc_final: 0.8515 (m110) REVERT: E 90 PHE cc_start: 0.8558 (t80) cc_final: 0.7453 (t80) REVERT: E 105 HIS cc_start: 0.8070 (t70) cc_final: 0.7371 (t70) REVERT: E 106 LEU cc_start: 0.9200 (mt) cc_final: 0.8885 (mt) REVERT: E 110 PHE cc_start: 0.7885 (m-80) cc_final: 0.7527 (m-80) REVERT: E 113 MET cc_start: 0.8930 (mtp) cc_final: 0.8507 (mtp) REVERT: E 134 GLU cc_start: 0.8864 (tt0) cc_final: 0.8655 (tm-30) REVERT: E 135 PHE cc_start: 0.8330 (m-10) cc_final: 0.7837 (m-80) REVERT: E 218 MET cc_start: 0.6778 (mtp) cc_final: 0.6544 (ptm) REVERT: E 220 MET cc_start: 0.8688 (mmm) cc_final: 0.7836 (mmm) REVERT: E 221 TRP cc_start: 0.7042 (t60) cc_final: 0.6700 (t60) REVERT: E 260 PHE cc_start: 0.8924 (m-80) cc_final: 0.8603 (m-80) REVERT: F 6 GLN cc_start: 0.8725 (mt0) cc_final: 0.8412 (tm-30) REVERT: F 141 ILE cc_start: 0.9086 (mt) cc_final: 0.8775 (mm) REVERT: F 168 LEU cc_start: 0.9203 (mt) cc_final: 0.8936 (mt) REVERT: F 169 ASN cc_start: 0.8544 (m-40) cc_final: 0.7749 (t0) REVERT: G 224 LEU cc_start: 0.8145 (mt) cc_final: 0.7749 (mt) REVERT: G 228 SER cc_start: 0.8251 (t) cc_final: 0.7905 (p) REVERT: G 242 TYR cc_start: 0.7801 (m-80) cc_final: 0.7530 (m-80) REVERT: G 255 TRP cc_start: 0.7864 (m100) cc_final: 0.7286 (m100) REVERT: G 256 VAL cc_start: 0.9261 (t) cc_final: 0.8968 (p) REVERT: H 242 TYR cc_start: 0.7048 (p90) cc_final: 0.6629 (p90) REVERT: H 258 ASP cc_start: 0.9244 (p0) cc_final: 0.8720 (p0) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2996 time to fit residues: 141.1153 Evaluate side-chains 200 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 52 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN A 154 GLN A 167 GLN B 79 HIS ** 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 E 154 GLN F 108 GLN F 192 ASN F 195 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.069614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.057822 restraints weight = 61060.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.059620 restraints weight = 35908.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.060905 restraints weight = 24186.905| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11986 Z= 0.253 Angle : 0.733 9.325 16630 Z= 0.404 Chirality : 0.045 0.172 1790 Planarity : 0.006 0.061 1856 Dihedral : 23.514 146.840 2160 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.10 % Allowed : 2.02 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1202 helix: 0.50 (0.24), residues: 422 sheet: -0.30 (0.41), residues: 154 loop : -0.86 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP F 208 HIS 0.011 0.002 HIS B 105 PHE 0.035 0.003 PHE E 72 TYR 0.021 0.003 TYR E 178 ARG 0.014 0.001 ARG B 94 Details of bonding type rmsd hydrogen bonds : bond 0.05899 ( 556) hydrogen bonds : angle 6.64317 ( 1484) metal coordination : bond 0.01245 ( 16) metal coordination : angle 5.13226 ( 6) covalent geometry : bond 0.00532 (11970) covalent geometry : angle 0.72673 (16624) *********************** 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 246 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 245 time to evaluate : 1.401 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: 0.9039 (mt0) cc_final: 0.8422 (mm110) REVERT: A 19 LEU cc_start: 0.9515 (mt) cc_final: 0.9218 (tp) REVERT: A 90 PHE cc_start: 0.8721 (t80) cc_final: 0.7367 (t80) REVERT: A 113 MET cc_start: 0.9118 (mtp) cc_final: 0.8813 (mtp) REVERT: A 118 LYS cc_start: 0.8013 (ptpt) cc_final: 0.7695 (tttm) REVERT: A 119 ILE cc_start: 0.8944 (tt) cc_final: 0.8438 (tt) REVERT: A 194 VAL cc_start: 0.8845 (t) cc_final: 0.6741 (t) REVERT: A 220 MET cc_start: 0.8693 (mmm) cc_final: 0.8276 (mmm) REVERT: A 221 TRP cc_start: 0.7628 (t60) cc_final: 0.6954 (t60) REVERT: B 97 GLU cc_start: 0.8543 (pm20) cc_final: 0.8161 (mm-30) REVERT: B 141 ILE cc_start: 0.9109 (mt) cc_final: 0.8821 (mm) REVERT: B 168 LEU cc_start: 0.9264 (mt) cc_final: 0.9004 (mt) REVERT: B 169 ASN cc_start: 0.8528 (m-40) cc_final: 0.7974 (t0) REVERT: B 189 PHE cc_start: 0.8983 (t80) cc_final: 0.8648 (t80) REVERT: C 224 LEU cc_start: 0.8954 (mp) cc_final: 0.8142 (mp) REVERT: C 256 VAL cc_start: 0.9431 (t) cc_final: 0.9108 (p) REVERT: D 221 TRP cc_start: 0.8773 (p-90) cc_final: 0.8476 (p-90) REVERT: D 245 VAL cc_start: 0.8984 (m) cc_final: 0.8603 (p) REVERT: E 6 GLN cc_start: 0.9085 (mt0) cc_final: 0.8627 (mm110) REVERT: E 19 LEU cc_start: 0.9396 (mt) cc_final: 0.9078 (tt) REVERT: E 25 ILE cc_start: 0.8825 (pt) cc_final: 0.8279 (pt) REVERT: E 29 GLN cc_start: 0.9216 (mt0) cc_final: 0.8679 (mm-40) REVERT: E 32 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8142 (mm-30) REVERT: E 79 HIS cc_start: 0.8260 (m170) cc_final: 0.7940 (m170) REVERT: E 90 PHE cc_start: 0.8576 (t80) cc_final: 0.7528 (t80) REVERT: E 105 HIS cc_start: 0.8517 (t70) cc_final: 0.8189 (t-90) REVERT: E 113 MET cc_start: 0.9064 (mtp) cc_final: 0.8617 (mtp) REVERT: E 134 GLU cc_start: 0.8988 (tt0) cc_final: 0.8693 (tm-30) REVERT: E 135 PHE cc_start: 0.8247 (m-10) cc_final: 0.7592 (m-80) REVERT: E 218 MET cc_start: 0.6916 (mtp) cc_final: 0.6670 (mtm) REVERT: E 220 MET cc_start: 0.8742 (mmm) cc_final: 0.8409 (tpp) REVERT: E 260 PHE cc_start: 0.8690 (m-80) cc_final: 0.8288 (m-80) REVERT: F 6 GLN cc_start: 0.8490 (mt0) cc_final: 0.8181 (tm-30) REVERT: F 139 TRP cc_start: 0.8857 (m-90) cc_final: 0.8505 (m-90) REVERT: F 141 ILE cc_start: 0.9042 (mt) cc_final: 0.8771 (mm) REVERT: F 168 LEU cc_start: 0.9236 (mt) cc_final: 0.8963 (mt) REVERT: F 169 ASN cc_start: 0.8662 (m-40) cc_final: 0.7824 (t0) REVERT: G 224 LEU cc_start: 0.8488 (mt) cc_final: 0.8194 (mt) REVERT: G 256 VAL cc_start: 0.9400 (t) cc_final: 0.9043 (p) REVERT: H 218 MET cc_start: 0.7367 (ttt) cc_final: 0.7161 (ttt) REVERT: H 221 TRP cc_start: 0.8650 (p-90) cc_final: 0.8206 (p-90) REVERT: H 242 TYR cc_start: 0.7449 (p90) cc_final: 0.7102 (p90) REVERT: H 258 ASP cc_start: 0.9312 (p0) cc_final: 0.8833 (p0) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.2850 time to fit residues: 105.0076 Evaluate side-chains 172 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.0370 chunk 35 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN 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 108 GLN ** 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 = 0.3368 r_free = 0.3368 target = 0.070875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.059322 restraints weight = 60523.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.061088 restraints weight = 36139.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.062349 restraints weight = 24502.556| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11986 Z= 0.171 Angle : 0.621 5.987 16630 Z= 0.344 Chirality : 0.042 0.161 1790 Planarity : 0.005 0.050 1856 Dihedral : 23.218 144.571 2160 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1202 helix: 0.72 (0.25), residues: 420 sheet: -0.30 (0.41), residues: 156 loop : -0.80 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 208 HIS 0.008 0.001 HIS B 13 PHE 0.019 0.002 PHE F 189 TYR 0.018 0.002 TYR E 178 ARG 0.005 0.001 ARG G 240 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 556) hydrogen bonds : angle 6.29009 ( 1484) metal coordination : bond 0.00771 ( 16) metal coordination : angle 4.32183 ( 6) covalent geometry : bond 0.00364 (11970) covalent geometry : angle 0.61526 (16624) *********************** 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 228 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 1.350 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: A 6 GLN cc_start: 0.8977 (mt0) cc_final: 0.8395 (mm110) REVERT: A 19 LEU cc_start: 0.9436 (mt) cc_final: 0.9097 (tt) REVERT: A 25 ILE cc_start: 0.8627 (pt) cc_final: 0.8349 (pt) REVERT: A 83 ASP cc_start: 0.8562 (t0) cc_final: 0.8309 (t0) REVERT: A 90 PHE cc_start: 0.8549 (t80) cc_final: 0.7691 (t80) REVERT: A 113 MET cc_start: 0.9146 (mtp) cc_final: 0.7761 (ttm) REVERT: A 220 MET cc_start: 0.8711 (mmm) cc_final: 0.8437 (tpp) REVERT: A 260 PHE cc_start: 0.8533 (m-80) cc_final: 0.8167 (m-10) REVERT: B 97 GLU cc_start: 0.8391 (pm20) cc_final: 0.8156 (mm-30) REVERT: B 110 PHE cc_start: 0.8322 (m-10) cc_final: 0.8102 (m-10) REVERT: B 141 ILE cc_start: 0.9004 (mt) cc_final: 0.8760 (mm) REVERT: B 168 LEU cc_start: 0.9275 (mt) cc_final: 0.9025 (mt) REVERT: B 169 ASN cc_start: 0.8641 (m-40) cc_final: 0.7892 (t0) REVERT: C 224 LEU cc_start: 0.8482 (mp) cc_final: 0.8139 (mp) REVERT: C 256 VAL cc_start: 0.9417 (t) cc_final: 0.9122 (p) REVERT: C 258 ASP cc_start: 0.7675 (p0) cc_final: 0.7467 (m-30) REVERT: E 6 GLN cc_start: 0.9028 (mt0) cc_final: 0.8541 (mm110) REVERT: E 19 LEU cc_start: 0.9488 (mt) cc_final: 0.9048 (tt) REVERT: E 25 ILE cc_start: 0.8868 (pt) cc_final: 0.8186 (pt) REVERT: E 29 GLN cc_start: 0.9116 (mt0) cc_final: 0.8692 (mm-40) REVERT: E 32 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8343 (mm-30) REVERT: E 56 LEU cc_start: 0.9111 (mm) cc_final: 0.8687 (pp) REVERT: E 79 HIS cc_start: 0.8033 (m170) cc_final: 0.7814 (m170) REVERT: E 90 PHE cc_start: 0.8506 (t80) cc_final: 0.7630 (t80) REVERT: E 105 HIS cc_start: 0.8140 (t70) cc_final: 0.7538 (t70) REVERT: E 106 LEU cc_start: 0.9170 (mt) cc_final: 0.8834 (mt) REVERT: E 110 PHE cc_start: 0.8871 (m-80) cc_final: 0.8255 (m-80) REVERT: E 113 MET cc_start: 0.9125 (mtp) cc_final: 0.8629 (mtp) REVERT: E 134 GLU cc_start: 0.8896 (tt0) cc_final: 0.8599 (tm-30) REVERT: E 135 PHE cc_start: 0.8015 (m-10) cc_final: 0.7554 (m-80) REVERT: E 218 MET cc_start: 0.6972 (mtp) cc_final: 0.6487 (ptm) REVERT: E 220 MET cc_start: 0.8805 (mmm) cc_final: 0.8086 (mmm) REVERT: E 221 TRP cc_start: 0.7544 (t60) cc_final: 0.7244 (t60) REVERT: E 260 PHE cc_start: 0.8627 (m-80) cc_final: 0.8350 (m-10) REVERT: F 139 TRP cc_start: 0.8708 (m-90) cc_final: 0.8170 (m-90) REVERT: F 141 ILE cc_start: 0.8938 (mt) cc_final: 0.8692 (mm) REVERT: F 168 LEU cc_start: 0.9308 (mt) cc_final: 0.9028 (mt) REVERT: F 169 ASN cc_start: 0.8593 (m-40) cc_final: 0.7730 (t0) REVERT: G 224 LEU cc_start: 0.8472 (mt) cc_final: 0.8155 (mt) REVERT: G 256 VAL cc_start: 0.9400 (t) cc_final: 0.9053 (p) REVERT: H 221 TRP cc_start: 0.8278 (p-90) cc_final: 0.7987 (p-90) REVERT: H 242 TYR cc_start: 0.7160 (p90) cc_final: 0.6868 (p90) REVERT: H 258 ASP cc_start: 0.9270 (p0) cc_final: 0.8826 (p0) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.2507 time to fit residues: 85.9994 Evaluate side-chains 164 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 167 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 161 HIS F 79 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.058354 restraints weight = 60398.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060159 restraints weight = 35753.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.061354 restraints weight = 24089.887| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11986 Z= 0.184 Angle : 0.625 7.343 16630 Z= 0.345 Chirality : 0.042 0.150 1790 Planarity : 0.005 0.044 1856 Dihedral : 23.169 140.998 2160 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1202 helix: 0.75 (0.25), residues: 424 sheet: -0.34 (0.41), residues: 156 loop : -0.76 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 208 HIS 0.010 0.001 HIS E 207 PHE 0.018 0.002 PHE F 189 TYR 0.018 0.002 TYR A 77 ARG 0.013 0.001 ARG F 94 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 556) hydrogen bonds : angle 6.28053 ( 1484) metal coordination : bond 0.00751 ( 16) metal coordination : angle 4.01495 ( 6) covalent geometry : bond 0.00396 (11970) covalent geometry : angle 0.62047 (16624) *********************** 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 226 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.370 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: 0.9102 (mt0) cc_final: 0.8511 (mm110) REVERT: A 19 LEU cc_start: 0.9454 (mt) cc_final: 0.9042 (tt) REVERT: A 25 ILE cc_start: 0.8541 (pt) cc_final: 0.8264 (pt) REVERT: A 90 PHE cc_start: 0.8642 (t80) cc_final: 0.7587 (t80) REVERT: A 113 MET cc_start: 0.9138 (mtp) cc_final: 0.8645 (mtp) REVERT: A 196 MET cc_start: 0.7870 (mmm) cc_final: 0.7648 (mmm) REVERT: A 260 PHE cc_start: 0.8575 (m-80) cc_final: 0.8366 (m-10) REVERT: B 141 ILE cc_start: 0.8936 (mt) cc_final: 0.8711 (mm) REVERT: B 168 LEU cc_start: 0.9299 (mt) cc_final: 0.9063 (mt) REVERT: B 169 ASN cc_start: 0.8634 (m-40) cc_final: 0.7969 (t0) REVERT: C 224 LEU cc_start: 0.8584 (mp) cc_final: 0.8247 (mp) REVERT: C 256 VAL cc_start: 0.9459 (t) cc_final: 0.9133 (p) REVERT: C 258 ASP cc_start: 0.7843 (p0) cc_final: 0.7567 (m-30) REVERT: E 6 GLN cc_start: 0.9174 (mt0) cc_final: 0.8714 (mm110) REVERT: E 19 LEU cc_start: 0.9521 (mt) cc_final: 0.9064 (tt) REVERT: E 25 ILE cc_start: 0.8752 (pt) cc_final: 0.8162 (pt) REVERT: E 29 GLN cc_start: 0.9206 (mt0) cc_final: 0.8718 (mm-40) REVERT: E 56 LEU cc_start: 0.9147 (mm) cc_final: 0.8708 (pp) REVERT: E 79 HIS cc_start: 0.8287 (m170) cc_final: 0.7799 (m170) REVERT: E 90 PHE cc_start: 0.8646 (t80) cc_final: 0.7787 (t80) REVERT: E 105 HIS cc_start: 0.8281 (t70) cc_final: 0.7974 (t70) REVERT: E 113 MET cc_start: 0.9003 (mtp) cc_final: 0.8422 (mtp) REVERT: E 134 GLU cc_start: 0.8976 (tt0) cc_final: 0.8633 (tm-30) REVERT: E 135 PHE cc_start: 0.8096 (m-10) cc_final: 0.7522 (m-80) REVERT: E 220 MET cc_start: 0.8810 (mmm) cc_final: 0.8221 (mpp) REVERT: F 139 TRP cc_start: 0.8671 (m-90) cc_final: 0.8210 (m-90) REVERT: F 141 ILE cc_start: 0.8778 (mt) cc_final: 0.8558 (mm) REVERT: F 168 LEU cc_start: 0.9354 (mt) cc_final: 0.9114 (mt) REVERT: F 169 ASN cc_start: 0.8581 (m-40) cc_final: 0.7838 (t0) REVERT: G 256 VAL cc_start: 0.9416 (t) cc_final: 0.9122 (p) REVERT: H 221 TRP cc_start: 0.8427 (p-90) cc_final: 0.7991 (p-90) REVERT: H 242 TYR cc_start: 0.7163 (p90) cc_final: 0.6924 (p90) REVERT: H 258 ASP cc_start: 0.9335 (p0) cc_final: 0.8904 (p0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2375 time to fit residues: 81.1489 Evaluate side-chains 156 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 4 optimal weight: 0.0970 chunk 111 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN ** 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 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060133 restraints weight = 60967.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.061946 restraints weight = 36577.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063260 restraints weight = 24691.800| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11986 Z= 0.136 Angle : 0.572 5.953 16630 Z= 0.316 Chirality : 0.041 0.138 1790 Planarity : 0.005 0.050 1856 Dihedral : 22.960 138.929 2160 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1202 helix: 0.96 (0.25), residues: 424 sheet: -0.20 (0.43), residues: 146 loop : -0.68 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 208 HIS 0.012 0.001 HIS E 161 PHE 0.015 0.001 PHE F 189 TYR 0.015 0.002 TYR F 127 ARG 0.007 0.000 ARG F 94 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 556) hydrogen bonds : angle 5.98922 ( 1484) metal coordination : bond 0.00561 ( 16) metal coordination : angle 3.65219 ( 6) covalent geometry : bond 0.00290 (11970) covalent geometry : angle 0.56807 (16624) *********************** 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 227 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.294 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: 0.9163 (mt0) cc_final: 0.8641 (mm110) REVERT: A 19 LEU cc_start: 0.9556 (mt) cc_final: 0.9014 (tp) REVERT: A 25 ILE cc_start: 0.8449 (pt) cc_final: 0.8241 (pt) REVERT: A 33 ILE cc_start: 0.9528 (mm) cc_final: 0.9207 (mm) REVERT: A 90 PHE cc_start: 0.8578 (t80) cc_final: 0.7535 (t80) REVERT: A 113 MET cc_start: 0.9016 (mtp) cc_final: 0.8553 (mtp) REVERT: A 188 LEU cc_start: 0.9535 (mt) cc_final: 0.9313 (mt) REVERT: A 196 MET cc_start: 0.8295 (mmm) cc_final: 0.7886 (mmm) REVERT: A 220 MET cc_start: 0.8741 (mmm) cc_final: 0.8315 (mmm) REVERT: A 260 PHE cc_start: 0.8495 (m-80) cc_final: 0.8259 (m-10) REVERT: B 110 PHE cc_start: 0.8545 (m-10) cc_final: 0.8268 (m-10) REVERT: B 141 ILE cc_start: 0.8853 (mt) cc_final: 0.8626 (mm) REVERT: B 168 LEU cc_start: 0.9294 (mt) cc_final: 0.9032 (mt) REVERT: B 169 ASN cc_start: 0.8634 (m-40) cc_final: 0.7989 (t0) REVERT: B 189 PHE cc_start: 0.8915 (t80) cc_final: 0.8668 (t80) REVERT: C 224 LEU cc_start: 0.8686 (mp) cc_final: 0.8276 (mp) REVERT: C 256 VAL cc_start: 0.9431 (t) cc_final: 0.9171 (p) REVERT: C 258 ASP cc_start: 0.7739 (p0) cc_final: 0.7490 (m-30) REVERT: E 6 GLN cc_start: 0.9162 (mt0) cc_final: 0.8725 (mm110) REVERT: E 19 LEU cc_start: 0.9491 (mt) cc_final: 0.9087 (tt) REVERT: E 25 ILE cc_start: 0.8667 (pt) cc_final: 0.8206 (pt) REVERT: E 29 GLN cc_start: 0.9143 (mt0) cc_final: 0.8666 (mm-40) REVERT: E 32 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8413 (mm-30) REVERT: E 56 LEU cc_start: 0.9181 (mm) cc_final: 0.8681 (pp) REVERT: E 79 HIS cc_start: 0.8154 (m170) cc_final: 0.7785 (m170) REVERT: E 90 PHE cc_start: 0.8497 (t80) cc_final: 0.7773 (t80) REVERT: E 106 LEU cc_start: 0.9271 (mt) cc_final: 0.9026 (mt) REVERT: E 110 PHE cc_start: 0.8979 (m-80) cc_final: 0.8473 (m-80) REVERT: E 113 MET cc_start: 0.8917 (mtp) cc_final: 0.8457 (mtp) REVERT: E 134 GLU cc_start: 0.8928 (tt0) cc_final: 0.8584 (tm-30) REVERT: E 135 PHE cc_start: 0.8047 (m-10) cc_final: 0.7384 (m-10) REVERT: E 196 MET cc_start: 0.8331 (mmm) cc_final: 0.7415 (tpp) REVERT: E 218 MET cc_start: 0.7068 (mtm) cc_final: 0.6413 (ptm) REVERT: E 220 MET cc_start: 0.8867 (mmm) cc_final: 0.8503 (tpp) REVERT: E 221 TRP cc_start: 0.8109 (t60) cc_final: 0.7307 (t60) REVERT: E 254 ILE cc_start: 0.8873 (mm) cc_final: 0.8622 (mm) REVERT: F 110 PHE cc_start: 0.8497 (m-10) cc_final: 0.8185 (m-10) REVERT: F 139 TRP cc_start: 0.8610 (m-90) cc_final: 0.8081 (m-90) REVERT: F 141 ILE cc_start: 0.8655 (mt) cc_final: 0.8407 (mm) REVERT: F 168 LEU cc_start: 0.9328 (mt) cc_final: 0.9088 (mt) REVERT: F 169 ASN cc_start: 0.8593 (m-40) cc_final: 0.7862 (t0) REVERT: G 224 LEU cc_start: 0.8511 (mp) cc_final: 0.7846 (mp) REVERT: H 221 TRP cc_start: 0.8352 (p-90) cc_final: 0.7992 (p-90) REVERT: H 258 ASP cc_start: 0.9337 (p0) cc_final: 0.8906 (p0) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2667 time to fit residues: 91.0840 Evaluate side-chains 155 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 111 optimal weight: 0.2980 chunk 95 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.059889 restraints weight = 60769.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.061714 restraints weight = 36225.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.063027 restraints weight = 24410.977| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11986 Z= 0.144 Angle : 0.587 6.898 16630 Z= 0.324 Chirality : 0.042 0.140 1790 Planarity : 0.005 0.044 1856 Dihedral : 22.883 138.303 2160 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1202 helix: 0.95 (0.25), residues: 424 sheet: -0.25 (0.42), residues: 148 loop : -0.71 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 208 HIS 0.010 0.001 HIS E 161 PHE 0.024 0.001 PHE F 135 TYR 0.016 0.002 TYR E 149 ARG 0.005 0.000 ARG F 94 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 556) hydrogen bonds : angle 5.98223 ( 1484) metal coordination : bond 0.00524 ( 16) metal coordination : angle 3.67325 ( 6) covalent geometry : bond 0.00307 (11970) covalent geometry : angle 0.58251 (16624) *********************** 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 216 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.119 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 6 GLN cc_start: 0.9226 (mt0) cc_final: 0.8760 (mm110) REVERT: A 15 ASN cc_start: 0.6651 (t0) cc_final: 0.6430 (t0) REVERT: A 19 LEU cc_start: 0.9573 (mt) cc_final: 0.9029 (tp) REVERT: A 33 ILE cc_start: 0.9529 (mm) cc_final: 0.9299 (mm) REVERT: A 90 PHE cc_start: 0.8513 (t80) cc_final: 0.7484 (t80) REVERT: A 113 MET cc_start: 0.9039 (mtp) cc_final: 0.8631 (mtp) REVERT: A 196 MET cc_start: 0.8270 (mmm) cc_final: 0.7969 (mmm) REVERT: A 220 MET cc_start: 0.8669 (mmm) cc_final: 0.8208 (mmm) REVERT: A 221 TRP cc_start: 0.7813 (t60) cc_final: 0.7573 (t60) REVERT: A 260 PHE cc_start: 0.8471 (m-80) cc_final: 0.8225 (m-10) REVERT: B 110 PHE cc_start: 0.8484 (m-10) cc_final: 0.8032 (m-10) REVERT: B 141 ILE cc_start: 0.8826 (mt) cc_final: 0.8577 (mm) REVERT: B 168 LEU cc_start: 0.9304 (mt) cc_final: 0.9044 (mt) REVERT: B 169 ASN cc_start: 0.8620 (m-40) cc_final: 0.7992 (t0) REVERT: B 189 PHE cc_start: 0.8854 (t80) cc_final: 0.8583 (t80) REVERT: C 224 LEU cc_start: 0.8722 (mp) cc_final: 0.8308 (mp) REVERT: C 256 VAL cc_start: 0.9421 (t) cc_final: 0.9142 (p) REVERT: C 258 ASP cc_start: 0.7815 (p0) cc_final: 0.7492 (m-30) REVERT: E 6 GLN cc_start: 0.9191 (mt0) cc_final: 0.8894 (mm110) REVERT: E 14 GLN cc_start: 0.7259 (tp40) cc_final: 0.6723 (tp40) REVERT: E 19 LEU cc_start: 0.9501 (mt) cc_final: 0.9109 (tt) REVERT: E 25 ILE cc_start: 0.8737 (pt) cc_final: 0.8219 (pt) REVERT: E 29 GLN cc_start: 0.9149 (mt0) cc_final: 0.8702 (mm-40) REVERT: E 56 LEU cc_start: 0.9180 (mm) cc_final: 0.8720 (pp) REVERT: E 79 HIS cc_start: 0.8262 (m170) cc_final: 0.7986 (m170) REVERT: E 83 ASP cc_start: 0.8732 (t0) cc_final: 0.8531 (t0) REVERT: E 90 PHE cc_start: 0.8493 (t80) cc_final: 0.7750 (t80) REVERT: E 106 LEU cc_start: 0.9327 (mt) cc_final: 0.8888 (mt) REVERT: E 110 PHE cc_start: 0.8986 (m-80) cc_final: 0.8276 (m-80) REVERT: E 113 MET cc_start: 0.8829 (mtp) cc_final: 0.8228 (mtp) REVERT: E 134 GLU cc_start: 0.8836 (tt0) cc_final: 0.8565 (tm-30) REVERT: E 135 PHE cc_start: 0.8055 (m-10) cc_final: 0.7127 (m-10) REVERT: E 196 MET cc_start: 0.8285 (mmm) cc_final: 0.7747 (mmm) REVERT: E 220 MET cc_start: 0.8835 (mmm) cc_final: 0.8476 (tpp) REVERT: F 110 PHE cc_start: 0.8556 (m-10) cc_final: 0.8253 (m-10) REVERT: F 139 TRP cc_start: 0.8732 (m-90) cc_final: 0.8330 (m-90) REVERT: F 141 ILE cc_start: 0.8551 (mt) cc_final: 0.8325 (mm) REVERT: F 168 LEU cc_start: 0.9332 (mt) cc_final: 0.9094 (mt) REVERT: F 169 ASN cc_start: 0.8601 (m-40) cc_final: 0.7900 (t0) REVERT: G 218 MET cc_start: 0.8343 (mpp) cc_final: 0.7903 (mpp) REVERT: G 224 LEU cc_start: 0.8476 (mp) cc_final: 0.8196 (mp) REVERT: G 256 VAL cc_start: 0.9351 (t) cc_final: 0.8955 (p) REVERT: H 242 TYR cc_start: 0.7421 (p90) cc_final: 0.7209 (p90) REVERT: H 258 ASP cc_start: 0.9276 (p0) cc_final: 0.8879 (p0) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1962 time to fit residues: 63.4585 Evaluate side-chains 152 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 0.1980 chunk 122 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 52 ASN ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS E 123 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.060980 restraints weight = 60334.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.062834 restraints weight = 35833.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.064088 restraints weight = 23932.074| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11986 Z= 0.131 Angle : 0.576 7.617 16630 Z= 0.317 Chirality : 0.042 0.165 1790 Planarity : 0.005 0.046 1856 Dihedral : 22.754 137.423 2160 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.10 % Allowed : 0.77 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1202 helix: 0.90 (0.25), residues: 424 sheet: -0.37 (0.39), residues: 178 loop : -0.63 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 208 HIS 0.009 0.001 HIS E 161 PHE 0.028 0.001 PHE B 135 TYR 0.014 0.002 TYR E 149 ARG 0.004 0.000 ARG F 94 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 556) hydrogen bonds : angle 5.87739 ( 1484) metal coordination : bond 0.00506 ( 16) metal coordination : angle 3.84597 ( 6) covalent geometry : bond 0.00280 (11970) covalent geometry : angle 0.57135 (16624) *********************** 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 223 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 3.085 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: A 6 GLN cc_start: 0.9235 (mt0) cc_final: 0.8648 (pt0) REVERT: A 19 LEU cc_start: 0.9599 (mt) cc_final: 0.9082 (tp) REVERT: A 25 ILE cc_start: 0.8519 (pt) cc_final: 0.8316 (pt) REVERT: A 72 PHE cc_start: 0.7208 (m-80) cc_final: 0.6895 (m-80) REVERT: A 83 ASP cc_start: 0.8449 (t0) cc_final: 0.7856 (t0) REVERT: A 90 PHE cc_start: 0.8449 (t80) cc_final: 0.7284 (t80) REVERT: A 106 LEU cc_start: 0.9245 (mt) cc_final: 0.9020 (mt) REVERT: A 113 MET cc_start: 0.9051 (mtp) cc_final: 0.8659 (mtp) REVERT: A 196 MET cc_start: 0.8467 (mmm) cc_final: 0.8166 (mmm) REVERT: A 220 MET cc_start: 0.8683 (mmm) cc_final: 0.8218 (mmm) REVERT: A 260 PHE cc_start: 0.8396 (m-80) cc_final: 0.8112 (m-10) REVERT: B 110 PHE cc_start: 0.8503 (m-10) cc_final: 0.8061 (m-10) REVERT: B 141 ILE cc_start: 0.8710 (mt) cc_final: 0.8509 (mm) REVERT: B 168 LEU cc_start: 0.9291 (mt) cc_final: 0.9037 (mt) REVERT: B 169 ASN cc_start: 0.8626 (m-40) cc_final: 0.8005 (t0) REVERT: B 189 PHE cc_start: 0.8796 (t80) cc_final: 0.8503 (t80) REVERT: C 224 LEU cc_start: 0.8669 (mp) cc_final: 0.7985 (mp) REVERT: C 256 VAL cc_start: 0.9446 (t) cc_final: 0.9210 (p) REVERT: E 6 GLN cc_start: 0.9200 (mt0) cc_final: 0.8966 (mm110) REVERT: E 14 GLN cc_start: 0.7343 (tp40) cc_final: 0.6664 (tp40) REVERT: E 19 LEU cc_start: 0.9503 (mt) cc_final: 0.9151 (tt) REVERT: E 25 ILE cc_start: 0.8708 (pt) cc_final: 0.8167 (pt) REVERT: E 29 GLN cc_start: 0.9140 (mt0) cc_final: 0.8690 (mm-40) REVERT: E 56 LEU cc_start: 0.9168 (mm) cc_final: 0.8712 (pp) REVERT: E 79 HIS cc_start: 0.8194 (m170) cc_final: 0.7912 (m170) REVERT: E 83 ASP cc_start: 0.8739 (t0) cc_final: 0.8492 (t0) REVERT: E 90 PHE cc_start: 0.8380 (t80) cc_final: 0.7745 (t80) REVERT: E 113 MET cc_start: 0.8797 (mtp) cc_final: 0.8451 (mtp) REVERT: E 134 GLU cc_start: 0.8813 (tt0) cc_final: 0.8568 (tm-30) REVERT: E 135 PHE cc_start: 0.7961 (m-10) cc_final: 0.7088 (m-10) REVERT: E 150 ASN cc_start: 0.8812 (t0) cc_final: 0.8565 (t0) REVERT: E 196 MET cc_start: 0.8443 (mmm) cc_final: 0.7897 (mmm) REVERT: E 220 MET cc_start: 0.8770 (mmm) cc_final: 0.8205 (mmm) REVERT: F 110 PHE cc_start: 0.8499 (m-10) cc_final: 0.8177 (m-10) REVERT: F 139 TRP cc_start: 0.8664 (m-90) cc_final: 0.8196 (m-90) REVERT: F 168 LEU cc_start: 0.9328 (mt) cc_final: 0.9084 (mt) REVERT: F 169 ASN cc_start: 0.8599 (m-40) cc_final: 0.7836 (t0) REVERT: H 258 ASP cc_start: 0.9142 (p0) cc_final: 0.8882 (p0) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.2551 time to fit residues: 85.9539 Evaluate side-chains 161 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS F 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.070027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.058779 restraints weight = 61629.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060551 restraints weight = 36868.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.061784 restraints weight = 24760.338| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11986 Z= 0.191 Angle : 0.648 8.815 16630 Z= 0.354 Chirality : 0.043 0.184 1790 Planarity : 0.005 0.038 1856 Dihedral : 22.847 138.008 2160 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1202 helix: 0.52 (0.25), residues: 426 sheet: -0.56 (0.37), residues: 188 loop : -0.67 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP E 208 HIS 0.008 0.002 HIS E 207 PHE 0.022 0.002 PHE A 135 TYR 0.019 0.002 TYR D 242 ARG 0.007 0.000 ARG F 206 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 556) hydrogen bonds : angle 6.31244 ( 1484) metal coordination : bond 0.01138 ( 16) metal coordination : angle 5.08984 ( 6) covalent geometry : bond 0.00407 (11970) covalent geometry : angle 0.64042 (16624) *********************** 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: 0 poor density : 202 time to evaluate : 1.177 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: 0.9143 (mt0) cc_final: 0.8801 (mm110) REVERT: A 15 ASN cc_start: 0.7345 (t0) cc_final: 0.6957 (t0) REVERT: A 19 LEU cc_start: 0.9670 (mt) cc_final: 0.9051 (tt) REVERT: A 25 ILE cc_start: 0.8597 (pt) cc_final: 0.8277 (pt) REVERT: A 33 ILE cc_start: 0.9554 (tp) cc_final: 0.9244 (tp) REVERT: A 83 ASP cc_start: 0.8765 (t0) cc_final: 0.8168 (t0) REVERT: A 90 PHE cc_start: 0.8640 (t80) cc_final: 0.7403 (t80) REVERT: A 113 MET cc_start: 0.8983 (mtp) cc_final: 0.8636 (mtp) REVERT: A 188 LEU cc_start: 0.9309 (mt) cc_final: 0.9101 (mt) REVERT: A 196 MET cc_start: 0.8219 (mmm) cc_final: 0.7679 (mmt) REVERT: A 220 MET cc_start: 0.8651 (mmm) cc_final: 0.8282 (mmm) REVERT: B 110 PHE cc_start: 0.8459 (m-10) cc_final: 0.8061 (m-10) REVERT: B 141 ILE cc_start: 0.8791 (mt) cc_final: 0.8586 (mm) REVERT: B 168 LEU cc_start: 0.9289 (mt) cc_final: 0.9011 (mt) REVERT: B 169 ASN cc_start: 0.8601 (m-40) cc_final: 0.8001 (t0) REVERT: C 224 LEU cc_start: 0.8715 (mp) cc_final: 0.8289 (mp) REVERT: C 256 VAL cc_start: 0.9458 (t) cc_final: 0.9137 (p) REVERT: E 6 GLN cc_start: 0.9215 (mt0) cc_final: 0.9008 (mm110) REVERT: E 14 GLN cc_start: 0.7542 (tp40) cc_final: 0.7043 (tp40) REVERT: E 56 LEU cc_start: 0.9224 (mm) cc_final: 0.8735 (pp) REVERT: E 79 HIS cc_start: 0.8222 (m170) cc_final: 0.7878 (m170) REVERT: E 83 ASP cc_start: 0.8942 (t0) cc_final: 0.8093 (t0) REVERT: E 90 PHE cc_start: 0.8464 (t80) cc_final: 0.7410 (t80) REVERT: E 113 MET cc_start: 0.8605 (mtp) cc_final: 0.8377 (mtp) REVERT: E 134 GLU cc_start: 0.8900 (tt0) cc_final: 0.8488 (tm-30) REVERT: E 135 PHE cc_start: 0.7930 (m-10) cc_final: 0.7378 (m-10) REVERT: E 188 LEU cc_start: 0.9256 (mt) cc_final: 0.9010 (mt) REVERT: E 196 MET cc_start: 0.8298 (mmm) cc_final: 0.7893 (mmm) REVERT: E 220 MET cc_start: 0.8702 (mmm) cc_final: 0.8153 (tpp) REVERT: F 139 TRP cc_start: 0.8714 (m-90) cc_final: 0.8160 (m-90) REVERT: F 168 LEU cc_start: 0.9327 (mt) cc_final: 0.9088 (mt) REVERT: F 169 ASN cc_start: 0.8566 (m-40) cc_final: 0.7875 (t0) REVERT: G 224 LEU cc_start: 0.8198 (mp) cc_final: 0.7811 (mp) REVERT: H 258 ASP cc_start: 0.9186 (p0) cc_final: 0.8944 (p0) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1925 time to fit residues: 58.4661 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 : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 1.9990 chunk 96 optimal weight: 0.0470 chunk 37 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 0.0270 chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 52 ASN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN F 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.073029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.061231 restraints weight = 59505.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.063122 restraints weight = 35173.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064476 restraints weight = 23409.731| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11986 Z= 0.128 Angle : 0.596 7.659 16630 Z= 0.326 Chirality : 0.043 0.292 1790 Planarity : 0.005 0.038 1856 Dihedral : 22.735 136.947 2160 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.10 % Allowed : 0.00 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1202 helix: 0.61 (0.25), residues: 426 sheet: -0.41 (0.38), residues: 190 loop : -0.62 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 208 HIS 0.009 0.001 HIS E 161 PHE 0.025 0.001 PHE F 135 TYR 0.013 0.001 TYR A 178 ARG 0.004 0.000 ARG F 94 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 556) hydrogen bonds : angle 6.01273 ( 1484) metal coordination : bond 0.00755 ( 16) metal coordination : angle 3.58657 ( 6) covalent geometry : bond 0.00270 (11970) covalent geometry : angle 0.59217 (16624) ********************** 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 221 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 1.141 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 15 ASN cc_start: 0.6643 (t0) cc_final: 0.6328 (t0) REVERT: A 19 LEU cc_start: 0.9607 (mt) cc_final: 0.9040 (tt) REVERT: A 25 ILE cc_start: 0.8518 (pt) cc_final: 0.8092 (pt) REVERT: A 33 ILE cc_start: 0.9504 (tp) cc_final: 0.9211 (tp) REVERT: A 72 PHE cc_start: 0.6878 (m-80) cc_final: 0.6543 (m-80) REVERT: A 77 TYR cc_start: 0.7626 (m-10) cc_final: 0.7148 (m-10) REVERT: A 83 ASP cc_start: 0.8511 (t0) cc_final: 0.7980 (t0) REVERT: A 90 PHE cc_start: 0.8481 (t80) cc_final: 0.7331 (t80) REVERT: A 113 MET cc_start: 0.9084 (mtp) cc_final: 0.8611 (mtp) REVERT: A 188 LEU cc_start: 0.9352 (mt) cc_final: 0.9129 (mt) REVERT: A 196 MET cc_start: 0.8260 (mmm) cc_final: 0.7745 (mmt) REVERT: A 220 MET cc_start: 0.8725 (mmm) cc_final: 0.8271 (mmm) REVERT: A 255 TRP cc_start: 0.9082 (m100) cc_final: 0.8700 (m100) REVERT: B 110 PHE cc_start: 0.8366 (m-10) cc_final: 0.8140 (m-10) REVERT: B 112 TYR cc_start: 0.8027 (m-80) cc_final: 0.7250 (m-80) REVERT: B 168 LEU cc_start: 0.9274 (mt) cc_final: 0.9048 (mt) REVERT: B 169 ASN cc_start: 0.8630 (m-40) cc_final: 0.8049 (t0) REVERT: B 218 MET cc_start: 0.7001 (mpp) cc_final: 0.6782 (mpp) REVERT: C 224 LEU cc_start: 0.8632 (mp) cc_final: 0.8214 (mp) REVERT: C 256 VAL cc_start: 0.9487 (t) cc_final: 0.9225 (p) REVERT: E 6 GLN cc_start: 0.9191 (mt0) cc_final: 0.8978 (mm110) REVERT: E 14 GLN cc_start: 0.7317 (tp40) cc_final: 0.6820 (tp40) REVERT: E 56 LEU cc_start: 0.9133 (mm) cc_final: 0.8644 (pp) REVERT: E 79 HIS cc_start: 0.8248 (m170) cc_final: 0.7981 (m170) REVERT: E 83 ASP cc_start: 0.8731 (t0) cc_final: 0.7897 (t0) REVERT: E 90 PHE cc_start: 0.8340 (t80) cc_final: 0.8131 (t80) REVERT: E 113 MET cc_start: 0.8594 (mtp) cc_final: 0.7958 (mtp) REVERT: E 134 GLU cc_start: 0.8709 (tt0) cc_final: 0.8421 (tm-30) REVERT: E 135 PHE cc_start: 0.7722 (m-10) cc_final: 0.7284 (m-10) REVERT: E 188 LEU cc_start: 0.9383 (mt) cc_final: 0.9160 (mt) REVERT: E 196 MET cc_start: 0.8370 (mmm) cc_final: 0.7938 (mmm) REVERT: E 220 MET cc_start: 0.8861 (mmm) cc_final: 0.8353 (mmm) REVERT: E 221 TRP cc_start: 0.7716 (t60) cc_final: 0.7493 (t60) REVERT: F 110 PHE cc_start: 0.8342 (m-10) cc_final: 0.8079 (m-10) REVERT: F 139 TRP cc_start: 0.8720 (m-90) cc_final: 0.8147 (m-90) REVERT: F 168 LEU cc_start: 0.9330 (mt) cc_final: 0.9088 (mt) REVERT: F 169 ASN cc_start: 0.8560 (m-40) cc_final: 0.7834 (t0) REVERT: F 189 PHE cc_start: 0.8904 (t80) cc_final: 0.8645 (t80) REVERT: G 224 LEU cc_start: 0.8626 (mp) cc_final: 0.8238 (mp) REVERT: H 242 TYR cc_start: 0.6986 (p90) cc_final: 0.6783 (p90) REVERT: H 258 ASP cc_start: 0.9126 (p0) cc_final: 0.8855 (p0) REVERT: H 261 ILE cc_start: 0.9181 (mm) cc_final: 0.8697 (mm) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.2172 time to fit residues: 70.4647 Evaluate side-chains 158 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 102 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 81 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN B 63 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN E 52 ASN F 192 ASN F 193 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.060892 restraints weight = 60266.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.062763 restraints weight = 35679.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.064064 restraints weight = 23840.047| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.6917 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= 0.132 Angle : 0.594 8.938 16630 Z= 0.325 Chirality : 0.042 0.197 1790 Planarity : 0.005 0.051 1856 Dihedral : 22.717 136.126 2160 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1202 helix: 0.53 (0.25), residues: 426 sheet: -0.20 (0.38), residues: 190 loop : -0.57 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 208 HIS 0.008 0.001 HIS E 161 PHE 0.018 0.001 PHE A 135 TYR 0.015 0.001 TYR A 178 ARG 0.015 0.000 ARG G 240 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 556) hydrogen bonds : angle 6.00895 ( 1484) metal coordination : bond 0.00513 ( 16) metal coordination : angle 3.48737 ( 6) covalent geometry : bond 0.00283 (11970) covalent geometry : angle 0.59023 (16624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4290.49 seconds wall clock time: 78 minutes 33.93 seconds (4713.93 seconds total)