Starting phenix.real_space_refine on Wed Sep 25 22:45:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/09_2024/3jca_6441.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/09_2024/3jca_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/09_2024/3jca_6441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/09_2024/3jca_6441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/09_2024/3jca_6441.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/09_2024/3jca_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.77, per 1000 atoms: 0.68 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: 3.03 Conformation dependent library (CDL) restraints added in 1.3 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: 4.65 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: 3.57 Time building geometry restraints manager: 3.49 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: 0.00 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.040 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- 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 : 0.012 0.062 11970 Z= 0.787 Angle : 1.491 12.509 16624 Z= 1.038 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 1.220 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: 0.2829 time to fit residues: 156.0744 Evaluate side-chains 227 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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: 0.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 11970 Z= 0.231 Angle : 0.655 6.423 16624 Z= 0.368 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.152 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 3 GLU cc_start: 0.8979 (pp20) cc_final: 0.8772 (pm20) REVERT: A 19 LEU cc_start: 0.9385 (mt) cc_final: 0.9098 (tt) REVERT: A 79 HIS cc_start: 0.8429 (m-70) cc_final: 0.8182 (m170) REVERT: A 90 PHE cc_start: 0.8783 (t80) cc_final: 0.7727 (t80) REVERT: A 105 HIS cc_start: 0.8258 (t70) cc_final: 0.7726 (t70) REVERT: A 113 MET cc_start: 0.9199 (mtp) cc_final: 0.8781 (mtp) REVERT: A 118 LYS cc_start: 0.8533 (ptpt) cc_final: 0.7885 (tttp) REVERT: A 119 ILE cc_start: 0.8818 (tt) cc_final: 0.8552 (tt) REVERT: A 145 THR cc_start: 0.6728 (p) cc_final: 0.6387 (t) REVERT: A 150 ASN cc_start: 0.8438 (t0) cc_final: 0.8193 (t0) REVERT: A 190 VAL cc_start: 0.9412 (t) cc_final: 0.9133 (t) REVERT: A 218 MET cc_start: 0.6998 (mtp) cc_final: 0.6766 (ptm) REVERT: A 223 ASP cc_start: 0.8126 (t0) cc_final: 0.7884 (t70) REVERT: A 260 PHE cc_start: 0.9000 (m-80) cc_final: 0.8565 (m-80) REVERT: B 6 GLN cc_start: 0.8751 (mt0) cc_final: 0.8389 (tm-30) REVERT: B 97 GLU cc_start: 0.8556 (pm20) cc_final: 0.8046 (mt-10) REVERT: B 101 ASP cc_start: 0.7716 (m-30) cc_final: 0.7385 (m-30) REVERT: B 141 ILE cc_start: 0.9134 (mt) cc_final: 0.8837 (mm) REVERT: B 168 LEU cc_start: 0.9297 (mt) cc_final: 0.9043 (mt) REVERT: B 169 ASN cc_start: 0.8647 (m-40) cc_final: 0.8262 (t0) REVERT: B 173 LYS cc_start: 0.7016 (mmtt) cc_final: 0.6554 (ptmt) REVERT: E 19 LEU cc_start: 0.9316 (mt) cc_final: 0.9081 (tt) REVERT: E 25 ILE cc_start: 0.8905 (pt) cc_final: 0.8444 (pt) REVERT: E 29 GLN cc_start: 0.9272 (mt0) cc_final: 0.8551 (mm-40) REVERT: E 32 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8806 (mm-30) REVERT: E 39 ASN cc_start: 0.8900 (m-40) cc_final: 0.8544 (m110) REVERT: E 69 VAL cc_start: 0.8103 (t) cc_final: 0.7804 (t) REVERT: E 79 HIS cc_start: 0.8358 (m-70) cc_final: 0.8146 (m170) REVERT: E 90 PHE cc_start: 0.8840 (t80) cc_final: 0.7779 (t80) REVERT: E 105 HIS cc_start: 0.8308 (t70) cc_final: 0.7593 (t70) REVERT: E 110 PHE cc_start: 0.8125 (m-80) cc_final: 0.7734 (m-80) REVERT: E 113 MET cc_start: 0.9167 (mtp) cc_final: 0.8747 (mtp) REVERT: E 134 GLU cc_start: 0.9012 (tt0) cc_final: 0.8718 (tm-30) REVERT: E 135 PHE cc_start: 0.8804 (m-10) cc_final: 0.8361 (m-80) REVERT: E 145 THR cc_start: 0.6366 (p) cc_final: 0.6132 (t) REVERT: E 218 MET cc_start: 0.6874 (mtp) cc_final: 0.6622 (ptm) REVERT: E 220 MET cc_start: 0.8747 (mmm) cc_final: 0.7890 (mmm) REVERT: E 221 TRP cc_start: 0.7280 (t60) cc_final: 0.6938 (t60) REVERT: E 260 PHE cc_start: 0.9005 (m-80) cc_final: 0.8595 (m-80) REVERT: F 6 GLN cc_start: 0.8854 (mt0) cc_final: 0.8443 (tm-30) REVERT: F 141 ILE cc_start: 0.9096 (mt) cc_final: 0.8803 (mm) REVERT: F 168 LEU cc_start: 0.9279 (mt) cc_final: 0.9020 (mt) REVERT: F 169 ASN cc_start: 0.8647 (m-40) cc_final: 0.7859 (t0) REVERT: G 224 LEU cc_start: 0.8280 (mt) cc_final: 0.7754 (mt) REVERT: G 228 SER cc_start: 0.8393 (t) cc_final: 0.8017 (p) REVERT: G 242 TYR cc_start: 0.7939 (m-80) cc_final: 0.7606 (m-80) REVERT: G 255 TRP cc_start: 0.8076 (m100) cc_final: 0.7479 (m100) REVERT: G 256 VAL cc_start: 0.9210 (t) cc_final: 0.8886 (p) REVERT: H 242 TYR cc_start: 0.7357 (p90) cc_final: 0.6930 (p90) REVERT: H 258 ASP cc_start: 0.9294 (p0) cc_final: 0.8730 (p0) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2183 time to fit residues: 99.9523 Evaluate side-chains 204 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 0.0000 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN A 167 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN B 201 HIS ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN F 192 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11970 Z= 0.200 Angle : 0.610 8.703 16624 Z= 0.339 Chirality : 0.042 0.134 1790 Planarity : 0.005 0.065 1856 Dihedral : 23.430 147.994 2160 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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: -0.17 (0.24), residues: 1202 helix: 0.72 (0.24), residues: 422 sheet: 0.03 (0.42), residues: 156 loop : -0.68 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 208 HIS 0.007 0.001 HIS B 207 PHE 0.033 0.002 PHE E 72 TYR 0.027 0.002 TYR B 112 ARG 0.009 0.001 ARG B 94 *********************** 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 280 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.332 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: A 6 GLN cc_start: 0.9209 (mt0) cc_final: 0.8648 (mm110) REVERT: A 19 LEU cc_start: 0.9403 (mt) cc_final: 0.9087 (tt) REVERT: A 90 PHE cc_start: 0.8783 (t80) cc_final: 0.7784 (t80) REVERT: A 113 MET cc_start: 0.9159 (mtp) cc_final: 0.8801 (mtp) REVERT: A 145 THR cc_start: 0.6429 (p) cc_final: 0.6140 (t) REVERT: A 218 MET cc_start: 0.6937 (mtp) cc_final: 0.6660 (ptm) REVERT: A 220 MET cc_start: 0.8554 (mmm) cc_final: 0.8183 (mmm) REVERT: A 223 ASP cc_start: 0.8242 (t0) cc_final: 0.8017 (t70) REVERT: A 260 PHE cc_start: 0.8925 (m-80) cc_final: 0.8377 (m-10) REVERT: B 97 GLU cc_start: 0.8591 (pm20) cc_final: 0.8058 (mt-10) REVERT: B 141 ILE cc_start: 0.9014 (mt) cc_final: 0.8696 (mm) REVERT: B 168 LEU cc_start: 0.9297 (mt) cc_final: 0.9038 (mt) REVERT: B 169 ASN cc_start: 0.8829 (m-40) cc_final: 0.8176 (t0) REVERT: C 224 LEU cc_start: 0.9006 (mp) cc_final: 0.7874 (mp) REVERT: C 256 VAL cc_start: 0.9292 (t) cc_final: 0.8896 (p) REVERT: C 261 ILE cc_start: 0.9290 (mm) cc_final: 0.9087 (mm) REVERT: D 245 VAL cc_start: 0.8881 (m) cc_final: 0.8667 (p) REVERT: E 6 GLN cc_start: 0.9174 (mt0) cc_final: 0.8837 (mm110) REVERT: E 25 ILE cc_start: 0.8867 (pt) cc_final: 0.8548 (pt) REVERT: E 29 GLN cc_start: 0.9282 (mt0) cc_final: 0.8741 (mm-40) REVERT: E 77 TYR cc_start: 0.7874 (m-10) cc_final: 0.7667 (m-10) REVERT: E 90 PHE cc_start: 0.8700 (t80) cc_final: 0.7733 (t80) REVERT: E 105 HIS cc_start: 0.8062 (t70) cc_final: 0.7680 (t70) REVERT: E 106 LEU cc_start: 0.9304 (mt) cc_final: 0.9043 (mt) REVERT: E 110 PHE cc_start: 0.8838 (m-80) cc_final: 0.8001 (m-80) REVERT: E 113 MET cc_start: 0.9238 (mtp) cc_final: 0.8732 (mtp) REVERT: E 134 GLU cc_start: 0.9072 (tt0) cc_final: 0.8405 (tm-30) REVERT: E 139 TRP cc_start: 0.7272 (m-90) cc_final: 0.6661 (m-90) REVERT: E 145 THR cc_start: 0.6995 (p) cc_final: 0.6697 (t) REVERT: E 190 VAL cc_start: 0.9297 (t) cc_final: 0.9051 (t) REVERT: E 218 MET cc_start: 0.6970 (mtp) cc_final: 0.6669 (ptm) REVERT: E 220 MET cc_start: 0.8761 (mmm) cc_final: 0.8481 (tpp) REVERT: E 221 TRP cc_start: 0.7526 (t60) cc_final: 0.7045 (t60) REVERT: E 260 PHE cc_start: 0.8909 (m-80) cc_final: 0.8696 (m-10) REVERT: F 6 GLN cc_start: 0.8708 (mt0) cc_final: 0.8305 (tm-30) REVERT: F 110 PHE cc_start: 0.8570 (m-10) cc_final: 0.8281 (m-10) REVERT: F 139 TRP cc_start: 0.8714 (m-90) cc_final: 0.8482 (m-90) REVERT: F 141 ILE cc_start: 0.8975 (mt) cc_final: 0.8659 (mm) REVERT: F 168 LEU cc_start: 0.9257 (mt) cc_final: 0.9001 (mt) REVERT: F 169 ASN cc_start: 0.8696 (m-40) cc_final: 0.7876 (t0) REVERT: G 224 LEU cc_start: 0.8552 (mt) cc_final: 0.8331 (mp) REVERT: G 225 LEU cc_start: 0.8850 (mt) cc_final: 0.8447 (mm) REVERT: G 256 VAL cc_start: 0.9334 (t) cc_final: 0.8984 (p) REVERT: H 218 MET cc_start: 0.7800 (ttt) cc_final: 0.7543 (ttt) REVERT: H 242 TYR cc_start: 0.7522 (p90) cc_final: 0.7129 (p90) REVERT: H 258 ASP cc_start: 0.9333 (p0) cc_final: 0.8795 (p0) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2235 time to fit residues: 90.1833 Evaluate side-chains 180 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 107 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 A 167 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 79 HIS F 192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11970 Z= 0.201 Angle : 0.589 6.412 16624 Z= 0.328 Chirality : 0.042 0.150 1790 Planarity : 0.005 0.045 1856 Dihedral : 23.219 145.088 2160 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: -0.00 (0.24), residues: 1202 helix: 0.76 (0.24), residues: 422 sheet: 0.19 (0.42), residues: 152 loop : -0.52 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 208 HIS 0.016 0.001 HIS A 105 PHE 0.032 0.002 PHE E 135 TYR 0.018 0.002 TYR F 112 ARG 0.015 0.001 ARG F 94 *********************** 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 246 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.567 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: A 6 GLN cc_start: 0.9225 (mt0) cc_final: 0.8682 (mm110) REVERT: A 19 LEU cc_start: 0.9415 (mt) cc_final: 0.9050 (tp) REVERT: A 90 PHE cc_start: 0.8914 (t80) cc_final: 0.7985 (t80) REVERT: A 113 MET cc_start: 0.9233 (mtp) cc_final: 0.8894 (mtp) REVERT: A 145 THR cc_start: 0.5267 (p) cc_final: 0.4973 (t) REVERT: A 171 LEU cc_start: 0.9610 (mm) cc_final: 0.9354 (mm) REVERT: A 196 MET cc_start: 0.8622 (mmm) cc_final: 0.8066 (mmm) REVERT: A 220 MET cc_start: 0.8598 (mmm) cc_final: 0.8272 (tpp) REVERT: A 260 PHE cc_start: 0.8824 (m-80) cc_final: 0.8603 (m-80) REVERT: B 19 LEU cc_start: 0.8250 (mt) cc_final: 0.7854 (mt) REVERT: B 97 GLU cc_start: 0.8569 (pm20) cc_final: 0.8077 (mt-10) REVERT: B 141 ILE cc_start: 0.8953 (mt) cc_final: 0.8703 (mm) REVERT: B 168 LEU cc_start: 0.9356 (mt) cc_final: 0.9088 (mt) REVERT: B 169 ASN cc_start: 0.8852 (m-40) cc_final: 0.8190 (t0) REVERT: B 220 MET cc_start: 0.7307 (mtm) cc_final: 0.6864 (mmm) REVERT: C 218 MET cc_start: 0.8678 (mpp) cc_final: 0.8008 (tpt) REVERT: C 224 LEU cc_start: 0.8467 (mp) cc_final: 0.7997 (mp) REVERT: C 256 VAL cc_start: 0.9338 (t) cc_final: 0.8898 (p) REVERT: D 245 VAL cc_start: 0.8951 (m) cc_final: 0.8656 (p) REVERT: E 6 GLN cc_start: 0.9238 (mt0) cc_final: 0.8979 (mm110) REVERT: E 29 GLN cc_start: 0.9198 (mt0) cc_final: 0.8838 (mm-40) REVERT: E 90 PHE cc_start: 0.8809 (t80) cc_final: 0.7891 (t80) REVERT: E 94 ARG cc_start: 0.8732 (mmm160) cc_final: 0.8453 (mmm-85) REVERT: E 105 HIS cc_start: 0.8029 (t70) cc_final: 0.7463 (t70) REVERT: E 106 LEU cc_start: 0.9321 (mt) cc_final: 0.9075 (mt) REVERT: E 110 PHE cc_start: 0.8891 (m-80) cc_final: 0.8002 (m-80) REVERT: E 113 MET cc_start: 0.9286 (mtp) cc_final: 0.8734 (mtp) REVERT: E 134 GLU cc_start: 0.9053 (tt0) cc_final: 0.8415 (tm-30) REVERT: E 145 THR cc_start: 0.6489 (p) cc_final: 0.6252 (t) REVERT: E 218 MET cc_start: 0.7143 (mtp) cc_final: 0.6888 (ptm) REVERT: E 220 MET cc_start: 0.8796 (mmm) cc_final: 0.8474 (tpp) REVERT: E 221 TRP cc_start: 0.7383 (t60) cc_final: 0.6908 (t60) REVERT: E 260 PHE cc_start: 0.8830 (m-80) cc_final: 0.8475 (m-10) REVERT: F 6 GLN cc_start: 0.8683 (mt0) cc_final: 0.8409 (pp30) REVERT: F 139 TRP cc_start: 0.8730 (m-90) cc_final: 0.8228 (m-90) REVERT: F 141 ILE cc_start: 0.8961 (mt) cc_final: 0.8744 (mt) REVERT: F 168 LEU cc_start: 0.9352 (mt) cc_final: 0.9079 (mt) REVERT: F 169 ASN cc_start: 0.8699 (m-40) cc_final: 0.7888 (t0) REVERT: G 225 LEU cc_start: 0.8852 (mt) cc_final: 0.8537 (mm) REVERT: G 256 VAL cc_start: 0.9348 (t) cc_final: 0.8979 (p) REVERT: H 218 MET cc_start: 0.8018 (ttt) cc_final: 0.7731 (ttt) REVERT: H 242 TYR cc_start: 0.7447 (p90) cc_final: 0.7056 (p90) REVERT: H 258 ASP cc_start: 0.9333 (p0) cc_final: 0.8831 (p0) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2059 time to fit residues: 75.6594 Evaluate side-chains 168 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 82 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 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 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 192 ASN F 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11970 Z= 0.264 Angle : 0.640 6.466 16624 Z= 0.354 Chirality : 0.043 0.224 1790 Planarity : 0.005 0.042 1856 Dihedral : 23.194 141.843 2160 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.10 % Allowed : 1.25 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.02 (0.24), residues: 1202 helix: 0.83 (0.25), residues: 424 sheet: -0.14 (0.40), residues: 158 loop : -0.51 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 208 HIS 0.012 0.002 HIS A 105 PHE 0.027 0.002 PHE B 189 TYR 0.016 0.002 TYR B 127 ARG 0.008 0.001 ARG F 94 *********************** 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 233 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.9249 (mt0) cc_final: 0.8693 (mm110) REVERT: A 19 LEU cc_start: 0.9447 (mt) cc_final: 0.9094 (tp) REVERT: A 56 LEU cc_start: 0.9438 (mm) cc_final: 0.8737 (tp) REVERT: A 77 TYR cc_start: 0.8340 (m-80) cc_final: 0.7889 (m-10) REVERT: A 79 HIS cc_start: 0.8667 (m170) cc_final: 0.8361 (m170) REVERT: A 90 PHE cc_start: 0.8891 (t80) cc_final: 0.8063 (t80) REVERT: A 113 MET cc_start: 0.9292 (mtp) cc_final: 0.8912 (mtp) REVERT: A 177 TYR cc_start: 0.7191 (m-10) cc_final: 0.6939 (m-10) REVERT: A 194 VAL cc_start: 0.9056 (t) cc_final: 0.7648 (t) REVERT: A 196 MET cc_start: 0.8587 (mmm) cc_final: 0.8085 (mmm) REVERT: A 220 MET cc_start: 0.8766 (mmm) cc_final: 0.8457 (tpp) REVERT: B 97 GLU cc_start: 0.8637 (pm20) cc_final: 0.8377 (mm-30) REVERT: B 141 ILE cc_start: 0.8932 (mt) cc_final: 0.8658 (mm) REVERT: B 168 LEU cc_start: 0.9403 (mt) cc_final: 0.9155 (mt) REVERT: B 169 ASN cc_start: 0.8736 (m-40) cc_final: 0.8173 (t0) REVERT: B 189 PHE cc_start: 0.9212 (t80) cc_final: 0.8867 (t80) REVERT: C 224 LEU cc_start: 0.8490 (mp) cc_final: 0.8005 (mp) REVERT: C 256 VAL cc_start: 0.9415 (t) cc_final: 0.9040 (p) REVERT: E 29 GLN cc_start: 0.9165 (mt0) cc_final: 0.8847 (mm-40) REVERT: E 79 HIS cc_start: 0.8411 (m170) cc_final: 0.8044 (m170) REVERT: E 90 PHE cc_start: 0.8785 (t80) cc_final: 0.8097 (t80) REVERT: E 105 HIS cc_start: 0.8469 (t70) cc_final: 0.7966 (t70) REVERT: E 113 MET cc_start: 0.9302 (mtp) cc_final: 0.8828 (mtp) REVERT: E 134 GLU cc_start: 0.9073 (tt0) cc_final: 0.8739 (tm-30) REVERT: E 135 PHE cc_start: 0.8324 (m-80) cc_final: 0.7683 (m-80) REVERT: E 218 MET cc_start: 0.7222 (mtp) cc_final: 0.6906 (ptm) REVERT: E 220 MET cc_start: 0.8910 (mmm) cc_final: 0.8588 (tpp) REVERT: E 221 TRP cc_start: 0.7623 (t60) cc_final: 0.7191 (t60) REVERT: E 260 PHE cc_start: 0.8815 (m-80) cc_final: 0.8506 (m-10) REVERT: F 139 TRP cc_start: 0.8698 (m-90) cc_final: 0.8333 (m-90) REVERT: F 168 LEU cc_start: 0.9392 (mt) cc_final: 0.9150 (mt) REVERT: F 169 ASN cc_start: 0.8711 (m-40) cc_final: 0.7926 (t0) REVERT: G 224 LEU cc_start: 0.8527 (mp) cc_final: 0.8170 (mp) REVERT: G 256 VAL cc_start: 0.9299 (t) cc_final: 0.8942 (p) REVERT: G 258 ASP cc_start: 0.8122 (p0) cc_final: 0.7787 (m-30) REVERT: H 218 MET cc_start: 0.8112 (ttt) cc_final: 0.7769 (ttt) REVERT: H 242 TYR cc_start: 0.7530 (p90) cc_final: 0.7213 (p90) REVERT: H 258 ASP cc_start: 0.9372 (p0) cc_final: 0.8863 (p0) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.2101 time to fit residues: 71.7627 Evaluate side-chains 157 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 68 HIS A 79 HIS ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN B 79 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN E 207 HIS F 192 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11970 Z= 0.273 Angle : 0.643 6.861 16624 Z= 0.359 Chirality : 0.043 0.155 1790 Planarity : 0.005 0.051 1856 Dihedral : 23.144 140.579 2160 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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: -0.26 (0.24), residues: 1202 helix: 0.73 (0.25), residues: 422 sheet: -0.36 (0.42), residues: 148 loop : -0.70 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 208 HIS 0.009 0.002 HIS A 105 PHE 0.021 0.002 PHE F 189 TYR 0.018 0.002 TYR E 77 ARG 0.005 0.000 ARG G 240 *********************** 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 215 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.494 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: A 6 GLN cc_start: 0.9310 (mt0) cc_final: 0.8767 (pt0) REVERT: A 15 ASN cc_start: 0.6969 (t0) cc_final: 0.6749 (t0) REVERT: A 72 PHE cc_start: 0.7220 (m-80) cc_final: 0.6967 (m-80) REVERT: A 77 TYR cc_start: 0.8361 (m-80) cc_final: 0.7719 (m-10) REVERT: A 79 HIS cc_start: 0.8810 (m-70) cc_final: 0.8529 (m170) REVERT: A 90 PHE cc_start: 0.8796 (t80) cc_final: 0.8225 (t80) REVERT: A 113 MET cc_start: 0.9223 (mtp) cc_final: 0.8641 (mtp) REVERT: A 196 MET cc_start: 0.8541 (mmm) cc_final: 0.8029 (mmm) REVERT: A 220 MET cc_start: 0.8808 (mmm) cc_final: 0.8238 (mmm) REVERT: A 260 PHE cc_start: 0.8699 (m-80) cc_final: 0.8469 (m-10) REVERT: B 97 GLU cc_start: 0.8517 (pm20) cc_final: 0.8237 (mm-30) REVERT: B 141 ILE cc_start: 0.8930 (mt) cc_final: 0.8667 (mm) REVERT: B 168 LEU cc_start: 0.9397 (mt) cc_final: 0.9172 (mt) REVERT: B 169 ASN cc_start: 0.8796 (m-40) cc_final: 0.8218 (t0) REVERT: C 224 LEU cc_start: 0.8574 (mp) cc_final: 0.8082 (mp) REVERT: C 256 VAL cc_start: 0.9441 (t) cc_final: 0.9097 (p) REVERT: C 258 ASP cc_start: 0.8138 (p0) cc_final: 0.7816 (m-30) REVERT: E 29 GLN cc_start: 0.9161 (mt0) cc_final: 0.8757 (mm-40) REVERT: E 79 HIS cc_start: 0.8649 (m170) cc_final: 0.8198 (m170) REVERT: E 90 PHE cc_start: 0.8796 (t80) cc_final: 0.8123 (t80) REVERT: E 105 HIS cc_start: 0.8732 (t70) cc_final: 0.8072 (t70) REVERT: E 113 MET cc_start: 0.9226 (mtp) cc_final: 0.8637 (mtp) REVERT: E 134 GLU cc_start: 0.9166 (tt0) cc_final: 0.8770 (tm-30) REVERT: E 135 PHE cc_start: 0.8192 (m-80) cc_final: 0.7474 (m-80) REVERT: E 196 MET cc_start: 0.8382 (mmm) cc_final: 0.7801 (mmm) REVERT: E 220 MET cc_start: 0.8882 (mmm) cc_final: 0.8280 (mpp) REVERT: E 221 TRP cc_start: 0.7968 (t60) cc_final: 0.7495 (t60) REVERT: E 260 PHE cc_start: 0.8631 (m-80) cc_final: 0.8416 (m-10) REVERT: F 127 TYR cc_start: 0.8251 (m-80) cc_final: 0.8003 (m-80) REVERT: F 139 TRP cc_start: 0.8623 (m-90) cc_final: 0.8181 (m-90) REVERT: F 168 LEU cc_start: 0.9395 (mt) cc_final: 0.9165 (mt) REVERT: F 169 ASN cc_start: 0.8644 (m-40) cc_final: 0.7919 (t0) REVERT: F 195 ASN cc_start: 0.8929 (t0) cc_final: 0.8665 (t0) REVERT: F 196 MET cc_start: 0.6945 (mtt) cc_final: 0.6702 (mtp) REVERT: G 224 LEU cc_start: 0.8560 (mp) cc_final: 0.8282 (mp) REVERT: G 256 VAL cc_start: 0.9310 (t) cc_final: 0.8964 (p) REVERT: G 258 ASP cc_start: 0.8139 (p0) cc_final: 0.7812 (m-30) REVERT: H 218 MET cc_start: 0.8157 (ttt) cc_final: 0.7813 (ttt) REVERT: H 242 TYR cc_start: 0.7370 (p90) cc_final: 0.7093 (p90) REVERT: H 258 ASP cc_start: 0.9418 (p0) cc_final: 0.8900 (p0) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2409 time to fit residues: 76.1963 Evaluate side-chains 146 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11970 Z= 0.182 Angle : 0.570 6.525 16624 Z= 0.319 Chirality : 0.042 0.140 1790 Planarity : 0.005 0.043 1856 Dihedral : 22.975 139.076 2160 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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 (0.24), residues: 1202 helix: 0.91 (0.25), residues: 424 sheet: -0.22 (0.42), residues: 148 loop : -0.64 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 208 HIS 0.009 0.001 HIS A 105 PHE 0.024 0.002 PHE B 264 TYR 0.014 0.002 TYR B 127 ARG 0.009 0.000 ARG H 259 *********************** 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 222 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.172 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: 0.9423 (mt0) cc_final: 0.8862 (pt0) REVERT: A 14 GLN cc_start: 0.7271 (mp10) cc_final: 0.7033 (pm20) REVERT: A 15 ASN cc_start: 0.7071 (t0) cc_final: 0.6739 (p0) REVERT: A 28 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 72 PHE cc_start: 0.7273 (m-80) cc_final: 0.6963 (m-80) REVERT: A 77 TYR cc_start: 0.8315 (m-80) cc_final: 0.7696 (m-10) REVERT: A 79 HIS cc_start: 0.8675 (m-70) cc_final: 0.8399 (m170) REVERT: A 90 PHE cc_start: 0.8724 (t80) cc_final: 0.8150 (t80) REVERT: A 113 MET cc_start: 0.9222 (mtp) cc_final: 0.8889 (mtp) REVERT: A 196 MET cc_start: 0.8455 (mmm) cc_final: 0.8136 (mmm) REVERT: A 220 MET cc_start: 0.8806 (mmm) cc_final: 0.8231 (mmm) REVERT: A 260 PHE cc_start: 0.8623 (m-80) cc_final: 0.8169 (m-10) REVERT: B 97 GLU cc_start: 0.8442 (pm20) cc_final: 0.8008 (mt-10) REVERT: B 141 ILE cc_start: 0.8784 (mt) cc_final: 0.8538 (mm) REVERT: B 168 LEU cc_start: 0.9396 (mt) cc_final: 0.9157 (mt) REVERT: B 169 ASN cc_start: 0.8800 (m-40) cc_final: 0.8235 (t0) REVERT: C 218 MET cc_start: 0.8851 (mpp) cc_final: 0.8631 (mpp) REVERT: C 224 LEU cc_start: 0.8481 (mp) cc_final: 0.7908 (mp) REVERT: C 256 VAL cc_start: 0.9443 (t) cc_final: 0.9155 (p) REVERT: C 258 ASP cc_start: 0.7997 (p0) cc_final: 0.7711 (m-30) REVERT: E 29 GLN cc_start: 0.9118 (mt0) cc_final: 0.8765 (mm-40) REVERT: E 79 HIS cc_start: 0.8546 (m170) cc_final: 0.8179 (m170) REVERT: E 90 PHE cc_start: 0.8741 (t80) cc_final: 0.8109 (t80) REVERT: E 105 HIS cc_start: 0.8283 (t70) cc_final: 0.7949 (t70) REVERT: E 106 LEU cc_start: 0.9352 (mt) cc_final: 0.9088 (mt) REVERT: E 110 PHE cc_start: 0.9042 (m-80) cc_final: 0.8617 (m-80) REVERT: E 113 MET cc_start: 0.9163 (mtp) cc_final: 0.8836 (mtp) REVERT: E 134 GLU cc_start: 0.9067 (tt0) cc_final: 0.8746 (tm-30) REVERT: E 135 PHE cc_start: 0.8177 (m-80) cc_final: 0.7551 (m-80) REVERT: E 194 VAL cc_start: 0.9041 (t) cc_final: 0.8813 (t) REVERT: E 220 MET cc_start: 0.8908 (mmm) cc_final: 0.8379 (mmm) REVERT: E 221 TRP cc_start: 0.7927 (t60) cc_final: 0.7296 (t60) REVERT: E 260 PHE cc_start: 0.8638 (m-80) cc_final: 0.8385 (m-10) REVERT: F 110 PHE cc_start: 0.8751 (m-10) cc_final: 0.8500 (m-10) REVERT: F 127 TYR cc_start: 0.8046 (m-80) cc_final: 0.7822 (m-80) REVERT: F 139 TRP cc_start: 0.8617 (m-90) cc_final: 0.8323 (m-90) REVERT: F 168 LEU cc_start: 0.9363 (mt) cc_final: 0.9134 (mt) REVERT: F 169 ASN cc_start: 0.8671 (m-40) cc_final: 0.7955 (t0) REVERT: F 195 ASN cc_start: 0.8853 (t0) cc_final: 0.8572 (t0) REVERT: F 196 MET cc_start: 0.6922 (mtt) cc_final: 0.6693 (mtp) REVERT: G 218 MET cc_start: 0.8904 (mpp) cc_final: 0.8681 (mpp) REVERT: G 224 LEU cc_start: 0.8469 (mp) cc_final: 0.8229 (mp) REVERT: G 256 VAL cc_start: 0.9363 (t) cc_final: 0.8966 (p) REVERT: G 258 ASP cc_start: 0.7986 (p0) cc_final: 0.7756 (m-30) REVERT: H 218 MET cc_start: 0.8228 (ttt) cc_final: 0.7930 (ttt) REVERT: H 258 ASP cc_start: 0.9351 (p0) cc_final: 0.8863 (p0) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2083 time to fit residues: 68.6785 Evaluate side-chains 153 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.0870 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11970 Z= 0.171 Angle : 0.571 8.150 16624 Z= 0.317 Chirality : 0.042 0.158 1790 Planarity : 0.005 0.069 1856 Dihedral : 22.857 137.999 2160 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.25), residues: 1202 helix: 0.81 (0.25), residues: 424 sheet: 0.00 (0.42), residues: 158 loop : -0.65 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 208 HIS 0.009 0.001 HIS A 105 PHE 0.031 0.001 PHE B 189 TYR 0.014 0.002 TYR E 149 ARG 0.010 0.000 ARG C 240 *********************** 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 227 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 1.289 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: 0.9419 (mt0) cc_final: 0.8811 (pt0) REVERT: A 28 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 72 PHE cc_start: 0.7302 (m-80) cc_final: 0.7004 (m-80) REVERT: A 77 TYR cc_start: 0.8489 (m-80) cc_final: 0.7773 (m-10) REVERT: A 90 PHE cc_start: 0.8729 (t80) cc_final: 0.8152 (t80) REVERT: A 188 LEU cc_start: 0.9510 (mt) cc_final: 0.9300 (mt) REVERT: A 196 MET cc_start: 0.8587 (mmm) cc_final: 0.8203 (mmm) REVERT: A 220 MET cc_start: 0.8793 (mmm) cc_final: 0.8174 (mmm) REVERT: A 260 PHE cc_start: 0.8625 (m-80) cc_final: 0.8118 (m-10) REVERT: B 141 ILE cc_start: 0.8650 (mt) cc_final: 0.8399 (mm) REVERT: B 168 LEU cc_start: 0.9377 (mt) cc_final: 0.9164 (mt) REVERT: B 169 ASN cc_start: 0.8736 (m-40) cc_final: 0.8195 (t0) REVERT: C 224 LEU cc_start: 0.8574 (mp) cc_final: 0.7931 (mp) REVERT: C 256 VAL cc_start: 0.9461 (t) cc_final: 0.9194 (p) REVERT: C 258 ASP cc_start: 0.7907 (p0) cc_final: 0.7615 (m-30) REVERT: E 28 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7548 (tm-30) REVERT: E 29 GLN cc_start: 0.9005 (mt0) cc_final: 0.8536 (mm-40) REVERT: E 79 HIS cc_start: 0.8406 (m170) cc_final: 0.8106 (m-70) REVERT: E 83 ASP cc_start: 0.8442 (t0) cc_final: 0.7991 (t0) REVERT: E 90 PHE cc_start: 0.8669 (t80) cc_final: 0.8033 (t80) REVERT: E 106 LEU cc_start: 0.9375 (mt) cc_final: 0.9115 (mt) REVERT: E 110 PHE cc_start: 0.9032 (m-80) cc_final: 0.8616 (m-80) REVERT: E 113 MET cc_start: 0.9032 (mtp) cc_final: 0.7210 (mtp) REVERT: E 134 GLU cc_start: 0.8989 (tt0) cc_final: 0.8704 (tm-30) REVERT: E 135 PHE cc_start: 0.8115 (m-80) cc_final: 0.7490 (m-80) REVERT: E 220 MET cc_start: 0.8961 (mmm) cc_final: 0.8448 (mmm) REVERT: E 221 TRP cc_start: 0.7904 (t60) cc_final: 0.7207 (t60) REVERT: F 110 PHE cc_start: 0.8749 (m-10) cc_final: 0.8513 (m-10) REVERT: F 139 TRP cc_start: 0.8561 (m-90) cc_final: 0.8320 (m-90) REVERT: F 168 LEU cc_start: 0.9361 (mt) cc_final: 0.9143 (mt) REVERT: F 169 ASN cc_start: 0.8653 (m-40) cc_final: 0.7891 (t0) REVERT: F 195 ASN cc_start: 0.8858 (t0) cc_final: 0.8647 (t0) REVERT: F 196 MET cc_start: 0.7115 (mtt) cc_final: 0.6885 (mtp) REVERT: G 224 LEU cc_start: 0.8747 (mp) cc_final: 0.8283 (mp) REVERT: G 256 VAL cc_start: 0.9353 (t) cc_final: 0.8954 (p) REVERT: H 218 MET cc_start: 0.8209 (ttt) cc_final: 0.7912 (ttt) REVERT: H 242 TYR cc_start: 0.7564 (p90) cc_final: 0.7350 (p90) REVERT: H 258 ASP cc_start: 0.9376 (p0) cc_final: 0.8937 (p0) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.2468 time to fit residues: 81.5284 Evaluate side-chains 152 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 105 optimal weight: 0.0980 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 ASN A 79 HIS ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.6492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11970 Z= 0.191 Angle : 0.586 6.281 16624 Z= 0.325 Chirality : 0.042 0.152 1790 Planarity : 0.005 0.060 1856 Dihedral : 22.776 137.642 2160 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.81 % 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: -0.15 (0.25), residues: 1202 helix: 0.79 (0.25), residues: 424 sheet: -0.34 (0.38), residues: 178 loop : -0.61 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP F 208 HIS 0.009 0.001 HIS A 105 PHE 0.026 0.002 PHE B 264 TYR 0.014 0.002 TYR B 127 ARG 0.015 0.001 ARG E 59 *********************** 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 212 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.9421 (mt0) cc_final: 0.8806 (pt0) REVERT: A 15 ASN cc_start: 0.6888 (t0) cc_final: 0.6555 (t0) REVERT: A 28 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7670 (tm-30) REVERT: A 33 ILE cc_start: 0.9540 (mm) cc_final: 0.9335 (mm) REVERT: A 59 ARG cc_start: 0.7677 (mtt90) cc_final: 0.7362 (mtt90) REVERT: A 72 PHE cc_start: 0.7305 (m-80) cc_final: 0.7083 (m-80) REVERT: A 77 TYR cc_start: 0.8518 (m-80) cc_final: 0.7720 (m-10) REVERT: A 79 HIS cc_start: 0.8659 (m-70) cc_final: 0.8415 (m170) REVERT: A 83 ASP cc_start: 0.8737 (t0) cc_final: 0.8336 (t0) REVERT: A 90 PHE cc_start: 0.8739 (t80) cc_final: 0.8353 (t80) REVERT: A 113 MET cc_start: 0.9190 (mtp) cc_final: 0.8210 (ttm) REVERT: A 188 LEU cc_start: 0.9526 (mt) cc_final: 0.9320 (mt) REVERT: A 196 MET cc_start: 0.8717 (mmm) cc_final: 0.8390 (mmm) REVERT: A 220 MET cc_start: 0.8758 (mmm) cc_final: 0.8127 (mmm) REVERT: A 221 TRP cc_start: 0.8302 (t60) cc_final: 0.7554 (t60) REVERT: A 260 PHE cc_start: 0.8589 (m-80) cc_final: 0.8146 (m-10) REVERT: B 141 ILE cc_start: 0.8693 (mt) cc_final: 0.8469 (mm) REVERT: B 168 LEU cc_start: 0.9368 (mt) cc_final: 0.9162 (mt) REVERT: B 169 ASN cc_start: 0.8795 (m-40) cc_final: 0.8252 (t0) REVERT: C 218 MET cc_start: 0.8382 (mmp) cc_final: 0.7819 (pmm) REVERT: C 224 LEU cc_start: 0.8488 (mp) cc_final: 0.7910 (mp) REVERT: C 256 VAL cc_start: 0.9474 (t) cc_final: 0.9188 (p) REVERT: D 258 ASP cc_start: 0.9415 (p0) cc_final: 0.9198 (p0) REVERT: E 29 GLN cc_start: 0.9015 (mt0) cc_final: 0.8666 (mm-40) REVERT: E 56 LEU cc_start: 0.9332 (mm) cc_final: 0.8589 (tp) REVERT: E 79 HIS cc_start: 0.8542 (m170) cc_final: 0.8277 (m-70) REVERT: E 83 ASP cc_start: 0.8539 (t0) cc_final: 0.7969 (t0) REVERT: E 90 PHE cc_start: 0.8739 (t80) cc_final: 0.8011 (t80) REVERT: E 106 LEU cc_start: 0.9381 (mt) cc_final: 0.9098 (mt) REVERT: E 110 PHE cc_start: 0.9037 (m-10) cc_final: 0.8590 (m-80) REVERT: E 113 MET cc_start: 0.8791 (mtp) cc_final: 0.8130 (mtp) REVERT: E 134 GLU cc_start: 0.8932 (tt0) cc_final: 0.8662 (tm-30) REVERT: E 135 PHE cc_start: 0.8098 (m-80) cc_final: 0.7464 (m-80) REVERT: E 150 ASN cc_start: 0.8850 (t0) cc_final: 0.8646 (t0) REVERT: E 220 MET cc_start: 0.8919 (mmm) cc_final: 0.8394 (mmm) REVERT: E 221 TRP cc_start: 0.7947 (t60) cc_final: 0.7233 (t60) REVERT: F 110 PHE cc_start: 0.8754 (m-10) cc_final: 0.8488 (m-10) REVERT: F 139 TRP cc_start: 0.8505 (m-90) cc_final: 0.8209 (m-90) REVERT: F 168 LEU cc_start: 0.9378 (mt) cc_final: 0.9133 (mt) REVERT: F 169 ASN cc_start: 0.8651 (m-40) cc_final: 0.7891 (t0) REVERT: F 189 PHE cc_start: 0.9034 (t80) cc_final: 0.8818 (t80) REVERT: F 191 LEU cc_start: 0.9313 (tt) cc_final: 0.9039 (pp) REVERT: F 195 ASN cc_start: 0.8767 (t0) cc_final: 0.8516 (t0) REVERT: G 224 LEU cc_start: 0.8659 (mp) cc_final: 0.8312 (mp) REVERT: G 256 VAL cc_start: 0.9338 (t) cc_final: 0.8896 (p) REVERT: H 218 MET cc_start: 0.8229 (ttt) cc_final: 0.7949 (ttt) REVERT: H 258 ASP cc_start: 0.9357 (p0) cc_final: 0.8892 (p0) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.1963 time to fit residues: 61.6072 Evaluate side-chains 151 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.0970 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 81 optimal weight: 0.4980 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 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 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11970 Z= 0.176 Angle : 0.569 5.899 16624 Z= 0.317 Chirality : 0.042 0.153 1790 Planarity : 0.005 0.049 1856 Dihedral : 22.715 137.082 2160 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.25), residues: 1202 helix: 0.86 (0.26), residues: 426 sheet: -0.19 (0.37), residues: 188 loop : -0.60 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 208 HIS 0.009 0.001 HIS A 105 PHE 0.026 0.001 PHE B 189 TYR 0.012 0.001 TYR A 178 ARG 0.007 0.000 ARG C 240 ********************** 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 217 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.6749 (t0) cc_final: 0.6481 (t0) REVERT: A 28 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 72 PHE cc_start: 0.7374 (m-80) cc_final: 0.7063 (m-80) REVERT: A 77 TYR cc_start: 0.8496 (m-80) cc_final: 0.8242 (m-10) REVERT: A 79 HIS cc_start: 0.8610 (m-70) cc_final: 0.8402 (m170) REVERT: A 83 ASP cc_start: 0.8705 (t0) cc_final: 0.8487 (t0) REVERT: A 90 PHE cc_start: 0.8736 (t80) cc_final: 0.8117 (t80) REVERT: A 196 MET cc_start: 0.8737 (mmm) cc_final: 0.8434 (mmm) REVERT: A 220 MET cc_start: 0.8785 (mmm) cc_final: 0.8341 (mmm) REVERT: A 221 TRP cc_start: 0.8418 (t60) cc_final: 0.7673 (t60) REVERT: A 260 PHE cc_start: 0.8490 (m-80) cc_final: 0.8040 (m-10) REVERT: B 141 ILE cc_start: 0.8568 (mt) cc_final: 0.8348 (mm) REVERT: B 168 LEU cc_start: 0.9344 (mt) cc_final: 0.9133 (mt) REVERT: B 169 ASN cc_start: 0.8706 (m-40) cc_final: 0.8202 (t0) REVERT: C 218 MET cc_start: 0.8457 (mmp) cc_final: 0.7850 (pmm) REVERT: C 224 LEU cc_start: 0.8570 (mp) cc_final: 0.7997 (mp) REVERT: C 256 VAL cc_start: 0.9452 (t) cc_final: 0.9136 (p) REVERT: E 28 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7592 (tm-30) REVERT: E 29 GLN cc_start: 0.9020 (mt0) cc_final: 0.8546 (mm-40) REVERT: E 79 HIS cc_start: 0.8507 (m170) cc_final: 0.8246 (m-70) REVERT: E 83 ASP cc_start: 0.8433 (t0) cc_final: 0.7928 (t0) REVERT: E 90 PHE cc_start: 0.8742 (t80) cc_final: 0.8049 (t80) REVERT: E 106 LEU cc_start: 0.9380 (mt) cc_final: 0.9095 (mt) REVERT: E 110 PHE cc_start: 0.9050 (m-10) cc_final: 0.8557 (m-80) REVERT: E 113 MET cc_start: 0.8885 (mtp) cc_final: 0.8171 (mtp) REVERT: E 121 THR cc_start: 0.7231 (p) cc_final: 0.6892 (t) REVERT: E 134 GLU cc_start: 0.8896 (tt0) cc_final: 0.8642 (tm-30) REVERT: E 135 PHE cc_start: 0.8051 (m-80) cc_final: 0.7423 (m-80) REVERT: E 188 LEU cc_start: 0.9502 (mt) cc_final: 0.9275 (mt) REVERT: E 220 MET cc_start: 0.8942 (mmm) cc_final: 0.8396 (mmm) REVERT: E 221 TRP cc_start: 0.7940 (t60) cc_final: 0.7250 (t60) REVERT: F 110 PHE cc_start: 0.8754 (m-10) cc_final: 0.8509 (m-10) REVERT: F 118 LYS cc_start: 0.7571 (pttp) cc_final: 0.7227 (ptpp) REVERT: F 127 TYR cc_start: 0.8429 (m-80) cc_final: 0.8199 (m-80) REVERT: F 139 TRP cc_start: 0.8493 (m-90) cc_final: 0.8154 (m-90) REVERT: F 168 LEU cc_start: 0.9373 (mt) cc_final: 0.9137 (mt) REVERT: F 169 ASN cc_start: 0.8634 (m-40) cc_final: 0.7885 (t0) REVERT: F 191 LEU cc_start: 0.9272 (tt) cc_final: 0.8971 (pp) REVERT: F 195 ASN cc_start: 0.8779 (t0) cc_final: 0.8490 (t0) REVERT: G 218 MET cc_start: 0.8255 (mmp) cc_final: 0.7613 (pmm) REVERT: G 224 LEU cc_start: 0.8707 (mp) cc_final: 0.8224 (mp) REVERT: G 256 VAL cc_start: 0.9332 (t) cc_final: 0.8820 (p) REVERT: G 261 ILE cc_start: 0.9324 (mm) cc_final: 0.9121 (mm) REVERT: H 218 MET cc_start: 0.8269 (ttt) cc_final: 0.8000 (ttt) REVERT: H 258 ASP cc_start: 0.9303 (p0) cc_final: 0.8976 (p0) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.1968 time to fit residues: 63.6888 Evaluate side-chains 150 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN A 52 ASN A 87 HIS ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.072916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.061096 restraints weight = 58199.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.062944 restraints weight = 34507.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.064250 restraints weight = 23104.059| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11970 Z= 0.173 Angle : 0.565 5.628 16624 Z= 0.313 Chirality : 0.042 0.154 1790 Planarity : 0.005 0.042 1856 Dihedral : 22.717 136.659 2160 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.10 % Allowed : 0.48 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.25), residues: 1202 helix: 0.86 (0.26), residues: 426 sheet: -0.10 (0.37), residues: 188 loop : -0.54 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 208 HIS 0.008 0.001 HIS A 105 PHE 0.022 0.001 PHE B 264 TYR 0.012 0.001 TYR A 178 ARG 0.007 0.000 ARG C 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2518.20 seconds wall clock time: 46 minutes 1.32 seconds (2761.32 seconds total)