Starting phenix.real_space_refine on Fri Mar 15 11:21:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/03_2024/3jca_6441.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/03_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_6441/03_2024/3jca_6441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/03_2024/3jca_6441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/03_2024/3jca_6441.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jca_6441/03_2024/3jca_6441.pdb" } 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 Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.20, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 5.04 Conformation dependent library (CDL) restraints added in 1.9 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: 4.16 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: 3.71 Time building geometry restraints manager: 5.43 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: 97.98 - 105.16: 702 105.16 - 112.34: 6161 112.34 - 119.52: 3811 119.52 - 126.71: 5512 126.71 - 133.89: 438 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 2.520 nonbonded pdb=" N GLU F 71 " pdb=" OE1 GLU F 71 " model vdw 2.373 2.520 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 2.440 nonbonded pdb=" O PHE D 264 " pdb=" OG1 THR D 265 " model vdw 2.481 2.440 ... (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 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.120 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 39.470 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.710 ------------------------------------------------------------------------------- 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 : 1.257 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: 0.2733 time to fit residues: 150.9391 Evaluate side-chains 227 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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: 0.9980 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 B 201 HIS ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11970 Z= 0.212 Angle : 0.635 6.560 16624 Z= 0.357 Chirality : 0.043 0.166 1790 Planarity : 0.006 0.067 1856 Dihedral : 23.773 150.448 2160 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.24), residues: 1202 helix: 0.47 (0.24), residues: 420 sheet: 0.39 (0.44), residues: 146 loop : -1.05 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 208 HIS 0.007 0.001 HIS F 182 PHE 0.021 0.002 PHE E 110 TYR 0.016 0.002 TYR A 77 ARG 0.005 0.000 ARG A 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 : 1.335 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: 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: 0.8981 (pp20) cc_final: 0.8774 (pm20) REVERT: A 19 LEU cc_start: 0.9377 (mt) cc_final: 0.9103 (tt) REVERT: A 25 ILE cc_start: 0.8774 (pt) cc_final: 0.8370 (pt) REVERT: A 28 GLU cc_start: 0.8430 (mp0) cc_final: 0.7691 (tm-30) REVERT: A 29 GLN cc_start: 0.9168 (mt0) cc_final: 0.8635 (mm-40) REVERT: A 79 HIS cc_start: 0.8461 (m-70) cc_final: 0.8161 (m170) REVERT: A 90 PHE cc_start: 0.8713 (t80) cc_final: 0.7668 (t80) REVERT: A 113 MET cc_start: 0.9236 (mtp) cc_final: 0.8900 (mtp) REVERT: A 150 ASN cc_start: 0.8430 (t0) cc_final: 0.8211 (t0) REVERT: A 190 VAL cc_start: 0.9426 (t) cc_final: 0.9161 (t) REVERT: A 220 MET cc_start: 0.8599 (tpp) cc_final: 0.8310 (tpp) REVERT: A 223 ASP cc_start: 0.7883 (t0) cc_final: 0.7584 (t70) REVERT: A 260 PHE cc_start: 0.8970 (m-80) cc_final: 0.8517 (m-80) REVERT: B 6 GLN cc_start: 0.8782 (mt0) cc_final: 0.8425 (tm-30) REVERT: B 97 GLU cc_start: 0.8497 (pm20) cc_final: 0.7936 (mt-10) REVERT: B 101 ASP cc_start: 0.7414 (m-30) cc_final: 0.7201 (m-30) REVERT: B 141 ILE cc_start: 0.9173 (mt) cc_final: 0.8883 (mm) REVERT: B 168 LEU cc_start: 0.9268 (mt) cc_final: 0.9004 (mt) REVERT: B 169 ASN cc_start: 0.8560 (m-40) cc_final: 0.8157 (t0) REVERT: B 173 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6542 (ptmt) REVERT: B 195 ASN cc_start: 0.8428 (m-40) cc_final: 0.7969 (t0) REVERT: C 224 LEU cc_start: 0.8730 (mp) cc_final: 0.7956 (mp) REVERT: E 19 LEU cc_start: 0.9313 (mt) cc_final: 0.9062 (tt) REVERT: E 28 GLU cc_start: 0.8071 (pm20) cc_final: 0.7627 (pm20) REVERT: E 29 GLN cc_start: 0.9261 (mt0) cc_final: 0.9025 (mt0) REVERT: E 39 ASN cc_start: 0.8897 (m-40) cc_final: 0.8553 (m110) REVERT: E 79 HIS cc_start: 0.8406 (m-70) cc_final: 0.8100 (m170) REVERT: E 90 PHE cc_start: 0.8767 (t80) cc_final: 0.7704 (t80) REVERT: E 110 PHE cc_start: 0.8109 (m-80) cc_final: 0.7532 (m-80) REVERT: E 113 MET cc_start: 0.9233 (mtp) cc_final: 0.8866 (mtp) REVERT: E 134 GLU cc_start: 0.9021 (tt0) cc_final: 0.8720 (tm-30) REVERT: E 135 PHE cc_start: 0.8797 (m-10) cc_final: 0.8463 (m-80) REVERT: E 145 THR cc_start: 0.6161 (p) cc_final: 0.5955 (t) REVERT: E 220 MET cc_start: 0.8803 (mmm) cc_final: 0.7954 (mmm) REVERT: E 221 TRP cc_start: 0.7223 (t60) cc_final: 0.6855 (t60) REVERT: E 260 PHE cc_start: 0.8956 (m-80) cc_final: 0.8522 (m-80) REVERT: F 6 GLN cc_start: 0.8833 (mt0) cc_final: 0.8429 (tm-30) REVERT: F 141 ILE cc_start: 0.9139 (mt) cc_final: 0.8843 (mm) REVERT: F 168 LEU cc_start: 0.9272 (mt) cc_final: 0.8956 (mt) REVERT: F 169 ASN cc_start: 0.8562 (m-40) cc_final: 0.7750 (t0) REVERT: G 228 SER cc_start: 0.8305 (t) cc_final: 0.7941 (p) REVERT: G 255 TRP cc_start: 0.7975 (m100) cc_final: 0.7524 (m100) REVERT: G 256 VAL cc_start: 0.9235 (t) cc_final: 0.8970 (p) REVERT: H 242 TYR cc_start: 0.7263 (p90) cc_final: 0.6825 (p90) REVERT: H 258 ASP cc_start: 0.9302 (p0) cc_final: 0.8723 (p0) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2230 time to fit residues: 103.2238 Evaluate side-chains 204 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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: 6.9990 chunk 34 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11970 Z= 0.194 Angle : 0.592 5.726 16624 Z= 0.331 Chirality : 0.042 0.133 1790 Planarity : 0.005 0.051 1856 Dihedral : 23.454 147.728 2160 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: -0.06 (0.24), residues: 1202 helix: 0.89 (0.25), residues: 420 sheet: 0.15 (0.40), residues: 170 loop : -0.73 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 208 HIS 0.007 0.001 HIS B 105 PHE 0.031 0.002 PHE E 72 TYR 0.022 0.002 TYR B 112 ARG 0.012 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 283 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.260 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: A 19 LEU cc_start: 0.9428 (mt) cc_final: 0.9159 (tt) REVERT: A 25 ILE cc_start: 0.8865 (pt) cc_final: 0.8458 (pt) REVERT: A 28 GLU cc_start: 0.8437 (mp0) cc_final: 0.7712 (tm-30) REVERT: A 29 GLN cc_start: 0.9192 (mt0) cc_final: 0.8619 (mm-40) REVERT: A 52 ASN cc_start: 0.8199 (t0) cc_final: 0.7735 (p0) REVERT: A 90 PHE cc_start: 0.8808 (t80) cc_final: 0.7761 (t80) REVERT: A 113 MET cc_start: 0.9137 (mtp) cc_final: 0.8800 (mtp) REVERT: A 145 THR cc_start: 0.6484 (p) cc_final: 0.6189 (t) REVERT: A 220 MET cc_start: 0.8897 (tpp) cc_final: 0.7942 (mmm) REVERT: A 221 TRP cc_start: 0.7662 (t60) cc_final: 0.7413 (t60) REVERT: A 260 PHE cc_start: 0.8780 (m-80) cc_final: 0.8380 (m-80) REVERT: B 97 GLU cc_start: 0.8621 (pm20) cc_final: 0.8046 (mt-10) REVERT: B 141 ILE cc_start: 0.9098 (mt) cc_final: 0.8800 (mm) REVERT: B 168 LEU cc_start: 0.9329 (mt) cc_final: 0.9073 (mt) REVERT: B 169 ASN cc_start: 0.8776 (m-40) cc_final: 0.8109 (t0) REVERT: C 224 LEU cc_start: 0.8677 (mp) cc_final: 0.7895 (mp) REVERT: C 256 VAL cc_start: 0.9175 (t) cc_final: 0.8872 (p) REVERT: C 261 ILE cc_start: 0.9288 (mm) cc_final: 0.9085 (mm) REVERT: D 245 VAL cc_start: 0.8894 (m) cc_final: 0.8459 (p) REVERT: E 3 GLU cc_start: 0.9036 (pp20) cc_final: 0.8755 (pm20) REVERT: E 6 GLN cc_start: 0.9181 (mt0) cc_final: 0.8919 (mm110) REVERT: E 19 LEU cc_start: 0.9291 (mt) cc_final: 0.9083 (tt) REVERT: E 28 GLU cc_start: 0.8063 (pm20) cc_final: 0.7597 (pm20) REVERT: E 29 GLN cc_start: 0.9263 (mt0) cc_final: 0.8908 (mt0) REVERT: E 90 PHE cc_start: 0.8777 (t80) cc_final: 0.7690 (t80) REVERT: E 94 ARG cc_start: 0.8766 (mmm160) cc_final: 0.8488 (mmt90) REVERT: E 106 LEU cc_start: 0.9279 (mt) cc_final: 0.9078 (mt) REVERT: E 110 PHE cc_start: 0.8757 (m-80) cc_final: 0.8025 (m-80) REVERT: E 113 MET cc_start: 0.9223 (mtp) cc_final: 0.8783 (mtp) REVERT: E 134 GLU cc_start: 0.9033 (tt0) cc_final: 0.8711 (tm-30) REVERT: E 135 PHE cc_start: 0.8681 (m-10) cc_final: 0.8077 (m-80) REVERT: E 145 THR cc_start: 0.6926 (p) cc_final: 0.6717 (t) REVERT: E 190 VAL cc_start: 0.9291 (t) cc_final: 0.9088 (t) REVERT: E 220 MET cc_start: 0.8763 (mmm) cc_final: 0.7966 (mmm) REVERT: E 221 TRP cc_start: 0.7251 (t60) cc_final: 0.6655 (t60) REVERT: F 6 GLN cc_start: 0.8705 (mt0) cc_final: 0.8418 (pp30) REVERT: F 139 TRP cc_start: 0.8771 (m-90) cc_final: 0.8549 (m-90) REVERT: F 141 ILE cc_start: 0.9124 (mt) cc_final: 0.8803 (mm) REVERT: F 168 LEU cc_start: 0.9316 (mt) cc_final: 0.9055 (mt) REVERT: F 169 ASN cc_start: 0.8562 (m-40) cc_final: 0.7742 (t0) REVERT: G 256 VAL cc_start: 0.9330 (t) cc_final: 0.9071 (p) REVERT: H 242 TYR cc_start: 0.7531 (p90) cc_final: 0.7121 (p90) REVERT: H 258 ASP cc_start: 0.9258 (p0) cc_final: 0.8732 (p0) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.2148 time to fit residues: 88.6352 Evaluate side-chains 188 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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: 0.9980 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 HIS ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11970 Z= 0.178 Angle : 0.562 6.340 16624 Z= 0.315 Chirality : 0.042 0.153 1790 Planarity : 0.005 0.041 1856 Dihedral : 23.066 144.100 2160 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.10 % Allowed : 1.35 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1202 helix: 1.05 (0.25), residues: 420 sheet: 0.94 (0.48), residues: 122 loop : -0.50 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 208 HIS 0.005 0.001 HIS F 12 PHE 0.024 0.002 PHE E 72 TYR 0.015 0.002 TYR E 178 ARG 0.011 0.000 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 257 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 1.219 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: A 6 GLN cc_start: 0.9221 (mt0) cc_final: 0.9000 (mm110) REVERT: A 19 LEU cc_start: 0.9416 (mt) cc_final: 0.9200 (tt) REVERT: A 28 GLU cc_start: 0.8449 (mp0) cc_final: 0.8152 (tm-30) REVERT: A 56 LEU cc_start: 0.9367 (mm) cc_final: 0.8805 (tp) REVERT: A 77 TYR cc_start: 0.8103 (m-10) cc_final: 0.7882 (m-10) REVERT: A 90 PHE cc_start: 0.8851 (t80) cc_final: 0.7943 (t80) REVERT: A 94 ARG cc_start: 0.8648 (mmm160) cc_final: 0.8028 (mmm-85) REVERT: A 113 MET cc_start: 0.9204 (mtp) cc_final: 0.8971 (mtp) REVERT: A 145 THR cc_start: 0.5411 (p) cc_final: 0.5186 (t) REVERT: A 220 MET cc_start: 0.8980 (tpp) cc_final: 0.8094 (mmm) REVERT: A 255 TRP cc_start: 0.9084 (m100) cc_final: 0.8736 (m100) REVERT: A 260 PHE cc_start: 0.8753 (m-80) cc_final: 0.8367 (m-10) REVERT: B 97 GLU cc_start: 0.8451 (pm20) cc_final: 0.7891 (mt-10) REVERT: B 141 ILE cc_start: 0.9022 (mt) cc_final: 0.8788 (mm) REVERT: B 168 LEU cc_start: 0.9346 (mt) cc_final: 0.9101 (mt) REVERT: B 169 ASN cc_start: 0.8755 (m-40) cc_final: 0.8073 (t0) REVERT: C 224 LEU cc_start: 0.8607 (mp) cc_final: 0.7857 (mp) REVERT: C 256 VAL cc_start: 0.9209 (t) cc_final: 0.8887 (p) REVERT: C 261 ILE cc_start: 0.9328 (mm) cc_final: 0.9115 (mm) REVERT: E 19 LEU cc_start: 0.9302 (mt) cc_final: 0.9090 (tt) REVERT: E 28 GLU cc_start: 0.7924 (pm20) cc_final: 0.7544 (pm20) REVERT: E 29 GLN cc_start: 0.9246 (mt0) cc_final: 0.8865 (mt0) REVERT: E 32 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9095 (mt-10) REVERT: E 90 PHE cc_start: 0.8735 (t80) cc_final: 0.7972 (t80) REVERT: E 110 PHE cc_start: 0.8726 (m-80) cc_final: 0.7769 (m-80) REVERT: E 113 MET cc_start: 0.9252 (mtp) cc_final: 0.8752 (mtp) REVERT: E 134 GLU cc_start: 0.9004 (tt0) cc_final: 0.8652 (tm-30) REVERT: E 135 PHE cc_start: 0.8709 (m-10) cc_final: 0.8254 (m-80) REVERT: E 220 MET cc_start: 0.8847 (mmm) cc_final: 0.8121 (mmm) REVERT: E 221 TRP cc_start: 0.7312 (t60) cc_final: 0.6743 (t60) REVERT: E 255 TRP cc_start: 0.9130 (m100) cc_final: 0.8842 (m100) REVERT: F 6 GLN cc_start: 0.8697 (mt0) cc_final: 0.8467 (pp30) REVERT: F 110 PHE cc_start: 0.8754 (m-10) cc_final: 0.8355 (m-10) REVERT: F 139 TRP cc_start: 0.8727 (m-90) cc_final: 0.8288 (m-90) REVERT: F 141 ILE cc_start: 0.9043 (mt) cc_final: 0.8812 (mt) REVERT: F 168 LEU cc_start: 0.9327 (mt) cc_final: 0.9049 (mt) REVERT: F 169 ASN cc_start: 0.8548 (m-40) cc_final: 0.7735 (t0) REVERT: G 224 LEU cc_start: 0.8789 (mt) cc_final: 0.8466 (mt) REVERT: G 256 VAL cc_start: 0.9326 (t) cc_final: 0.9073 (p) REVERT: H 242 TYR cc_start: 0.7418 (p90) cc_final: 0.6988 (p90) REVERT: H 258 ASP cc_start: 0.9292 (p0) cc_final: 0.8776 (p0) outliers start: 1 outliers final: 1 residues processed: 256 average time/residue: 0.2036 time to fit residues: 76.9128 Evaluate side-chains 174 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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: 9.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 89 optimal weight: 0.0470 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 82 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN E 6 GLN ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN F 192 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5007 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= 0.184 Angle : 0.564 5.615 16624 Z= 0.313 Chirality : 0.041 0.180 1790 Planarity : 0.005 0.120 1856 Dihedral : 22.928 141.412 2160 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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: 0.35 (0.25), residues: 1202 helix: 1.13 (0.25), residues: 422 sheet: 0.33 (0.43), residues: 146 loop : -0.35 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 208 HIS 0.005 0.001 HIS F 13 PHE 0.036 0.002 PHE E 72 TYR 0.014 0.002 TYR A 178 ARG 0.006 0.000 ARG E 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 252 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.180 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: 0.9254 (mt0) cc_final: 0.9046 (mm110) REVERT: A 19 LEU cc_start: 0.9428 (mt) cc_final: 0.9215 (tt) REVERT: A 28 GLU cc_start: 0.8498 (mp0) cc_final: 0.8191 (tm-30) REVERT: A 90 PHE cc_start: 0.8691 (t80) cc_final: 0.7978 (t80) REVERT: A 94 ARG cc_start: 0.8594 (mmm160) cc_final: 0.7947 (mmm-85) REVERT: A 113 MET cc_start: 0.9278 (mtp) cc_final: 0.8914 (mtp) REVERT: A 145 THR cc_start: 0.5339 (p) cc_final: 0.5089 (t) REVERT: A 194 VAL cc_start: 0.8855 (t) cc_final: 0.7257 (t) REVERT: A 196 MET cc_start: 0.8227 (mmm) cc_final: 0.7389 (tpp) REVERT: A 220 MET cc_start: 0.9093 (tpp) cc_final: 0.8370 (mmm) REVERT: A 255 TRP cc_start: 0.9068 (m100) cc_final: 0.8646 (m100) REVERT: A 260 PHE cc_start: 0.8535 (m-80) cc_final: 0.8227 (m-80) REVERT: B 97 GLU cc_start: 0.8562 (pm20) cc_final: 0.7893 (mt-10) REVERT: B 110 PHE cc_start: 0.8653 (m-10) cc_final: 0.8432 (m-10) REVERT: B 141 ILE cc_start: 0.9030 (mt) cc_final: 0.8790 (mm) REVERT: B 168 LEU cc_start: 0.9386 (mt) cc_final: 0.9122 (mt) REVERT: B 169 ASN cc_start: 0.8694 (m-40) cc_final: 0.8022 (t0) REVERT: B 189 PHE cc_start: 0.9183 (t80) cc_final: 0.8789 (t80) REVERT: B 220 MET cc_start: 0.7813 (tpp) cc_final: 0.7437 (tpp) REVERT: C 224 LEU cc_start: 0.8635 (mp) cc_final: 0.8022 (mp) REVERT: C 256 VAL cc_start: 0.9245 (t) cc_final: 0.8938 (p) REVERT: C 261 ILE cc_start: 0.9345 (mm) cc_final: 0.9113 (mm) REVERT: D 245 VAL cc_start: 0.8978 (m) cc_final: 0.8550 (p) REVERT: E 19 LEU cc_start: 0.9340 (mt) cc_final: 0.9002 (tt) REVERT: E 25 ILE cc_start: 0.8897 (pt) cc_final: 0.8603 (pt) REVERT: E 32 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8993 (mm-30) REVERT: E 77 TYR cc_start: 0.8449 (m-80) cc_final: 0.7946 (m-10) REVERT: E 90 PHE cc_start: 0.8501 (t80) cc_final: 0.7955 (t80) REVERT: E 106 LEU cc_start: 0.9295 (mt) cc_final: 0.9011 (mt) REVERT: E 110 PHE cc_start: 0.8946 (m-80) cc_final: 0.8346 (m-80) REVERT: E 113 MET cc_start: 0.9241 (mtp) cc_final: 0.8808 (mtp) REVERT: E 134 GLU cc_start: 0.9019 (tt0) cc_final: 0.8643 (tm-30) REVERT: E 135 PHE cc_start: 0.8636 (m-10) cc_final: 0.8244 (m-10) REVERT: E 220 MET cc_start: 0.8861 (mmm) cc_final: 0.8142 (mmm) REVERT: E 221 TRP cc_start: 0.7371 (t60) cc_final: 0.6676 (t60) REVERT: E 260 PHE cc_start: 0.8809 (m-80) cc_final: 0.8548 (m-80) REVERT: F 139 TRP cc_start: 0.8676 (m-90) cc_final: 0.8360 (m-90) REVERT: F 141 ILE cc_start: 0.8989 (mt) cc_final: 0.8770 (mm) REVERT: F 168 LEU cc_start: 0.9372 (mt) cc_final: 0.9123 (mt) REVERT: F 169 ASN cc_start: 0.8504 (m-40) cc_final: 0.7615 (t0) REVERT: G 224 LEU cc_start: 0.8803 (mt) cc_final: 0.8438 (mt) REVERT: G 256 VAL cc_start: 0.9349 (t) cc_final: 0.9084 (p) REVERT: G 261 ILE cc_start: 0.9296 (mm) cc_final: 0.9082 (mm) REVERT: H 235 LEU cc_start: 0.9142 (tp) cc_final: 0.8841 (tp) REVERT: H 242 TYR cc_start: 0.7501 (p90) cc_final: 0.7079 (p90) REVERT: H 258 ASP cc_start: 0.9362 (p0) cc_final: 0.8871 (p0) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1924 time to fit residues: 72.2898 Evaluate side-chains 167 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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: 6.9990 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN ** A 167 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 68 HIS ** E 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS F 79 HIS ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN F 195 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11970 Z= 0.290 Angle : 0.657 6.920 16624 Z= 0.368 Chirality : 0.043 0.161 1790 Planarity : 0.006 0.120 1856 Dihedral : 23.087 140.560 2160 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 0.84 (0.25), residues: 424 sheet: 0.30 (0.47), residues: 128 loop : -0.61 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP F 208 HIS 0.009 0.002 HIS F 13 PHE 0.037 0.003 PHE E 72 TYR 0.020 0.002 TYR A 77 ARG 0.006 0.001 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 222 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.105 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 28 GLU cc_start: 0.8575 (mp0) cc_final: 0.8105 (tm-30) REVERT: A 90 PHE cc_start: 0.8750 (t80) cc_final: 0.7976 (t80) REVERT: A 113 MET cc_start: 0.9132 (mtp) cc_final: 0.8708 (mtp) REVERT: A 196 MET cc_start: 0.8473 (mmm) cc_final: 0.8035 (mmm) REVERT: A 220 MET cc_start: 0.9087 (tpp) cc_final: 0.8355 (mmm) REVERT: B 97 GLU cc_start: 0.8684 (pm20) cc_final: 0.8262 (mm-30) REVERT: B 110 PHE cc_start: 0.8508 (m-10) cc_final: 0.8232 (m-10) REVERT: B 141 ILE cc_start: 0.9064 (mt) cc_final: 0.8837 (mm) REVERT: B 168 LEU cc_start: 0.9453 (mt) cc_final: 0.9201 (mt) REVERT: B 169 ASN cc_start: 0.8719 (m-40) cc_final: 0.8174 (t0) REVERT: C 224 LEU cc_start: 0.8727 (mp) cc_final: 0.8224 (mp) REVERT: C 256 VAL cc_start: 0.9243 (t) cc_final: 0.8961 (p) REVERT: D 218 MET cc_start: 0.8733 (tpt) cc_final: 0.8336 (tpp) REVERT: D 245 VAL cc_start: 0.9166 (m) cc_final: 0.8700 (p) REVERT: E 19 LEU cc_start: 0.9478 (mt) cc_final: 0.9175 (tt) REVERT: E 25 ILE cc_start: 0.8863 (pt) cc_final: 0.8627 (pt) REVERT: E 32 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8983 (mm-30) REVERT: E 77 TYR cc_start: 0.8512 (m-80) cc_final: 0.7981 (m-10) REVERT: E 90 PHE cc_start: 0.8721 (t80) cc_final: 0.7931 (t80) REVERT: E 113 MET cc_start: 0.9195 (mtp) cc_final: 0.8799 (mtp) REVERT: E 134 GLU cc_start: 0.9070 (tt0) cc_final: 0.8607 (tm-30) REVERT: E 135 PHE cc_start: 0.8605 (m-10) cc_final: 0.8182 (m-80) REVERT: E 194 VAL cc_start: 0.8834 (t) cc_final: 0.6985 (t) REVERT: E 196 MET cc_start: 0.8399 (mmm) cc_final: 0.8164 (mmm) REVERT: E 220 MET cc_start: 0.8862 (mmm) cc_final: 0.8314 (mpp) REVERT: E 221 TRP cc_start: 0.7841 (t60) cc_final: 0.7406 (t60) REVERT: F 118 LYS cc_start: 0.7212 (pttm) cc_final: 0.6982 (ptpp) REVERT: F 121 THR cc_start: 0.8062 (p) cc_final: 0.7324 (p) REVERT: F 127 TYR cc_start: 0.8462 (m-80) cc_final: 0.7784 (m-80) REVERT: F 139 TRP cc_start: 0.8642 (m-90) cc_final: 0.8141 (m-90) REVERT: F 141 ILE cc_start: 0.8962 (mt) cc_final: 0.8741 (mm) REVERT: F 168 LEU cc_start: 0.9418 (mt) cc_final: 0.9153 (mt) REVERT: F 169 ASN cc_start: 0.8500 (m-40) cc_final: 0.7759 (t0) REVERT: G 224 LEU cc_start: 0.9151 (mt) cc_final: 0.8512 (mt) REVERT: G 256 VAL cc_start: 0.9371 (t) cc_final: 0.9099 (p) REVERT: H 242 TYR cc_start: 0.7433 (p90) cc_final: 0.7148 (p90) REVERT: H 258 ASP cc_start: 0.9519 (p0) cc_final: 0.9122 (p0) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1898 time to fit residues: 63.3788 Evaluate side-chains 152 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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: 0.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 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 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11970 Z= 0.181 Angle : 0.578 7.520 16624 Z= 0.321 Chirality : 0.042 0.179 1790 Planarity : 0.005 0.106 1856 Dihedral : 22.852 139.629 2160 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.25), residues: 1202 helix: 1.04 (0.26), residues: 422 sheet: 0.16 (0.44), residues: 138 loop : -0.49 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 208 HIS 0.007 0.001 HIS F 79 PHE 0.029 0.002 PHE B 264 TYR 0.022 0.002 TYR F 127 ARG 0.004 0.000 ARG E 94 *********************** 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 215 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9231 (mm) cc_final: 0.9019 (mt) REVERT: A 28 GLU cc_start: 0.8636 (mp0) cc_final: 0.8254 (tm-30) REVERT: A 72 PHE cc_start: 0.7331 (m-80) cc_final: 0.7082 (m-80) REVERT: A 77 TYR cc_start: 0.7938 (m-10) cc_final: 0.7660 (m-10) REVERT: A 90 PHE cc_start: 0.8638 (t80) cc_final: 0.7851 (t80) REVERT: A 113 MET cc_start: 0.9225 (mtp) cc_final: 0.8812 (mtp) REVERT: A 196 MET cc_start: 0.8428 (mmm) cc_final: 0.7914 (mmm) REVERT: A 220 MET cc_start: 0.9095 (tpp) cc_final: 0.8475 (mmm) REVERT: A 221 TRP cc_start: 0.7645 (t60) cc_final: 0.7371 (t60) REVERT: B 97 GLU cc_start: 0.8535 (pm20) cc_final: 0.8199 (mm-30) REVERT: B 110 PHE cc_start: 0.8527 (m-10) cc_final: 0.8083 (m-10) REVERT: B 141 ILE cc_start: 0.8969 (mt) cc_final: 0.8739 (mm) REVERT: B 168 LEU cc_start: 0.9399 (mt) cc_final: 0.9173 (mt) REVERT: B 169 ASN cc_start: 0.8702 (m-40) cc_final: 0.8136 (t0) REVERT: C 256 VAL cc_start: 0.9304 (t) cc_final: 0.9036 (p) REVERT: D 245 VAL cc_start: 0.9161 (m) cc_final: 0.8669 (p) REVERT: E 19 LEU cc_start: 0.9511 (mt) cc_final: 0.9154 (tt) REVERT: E 25 ILE cc_start: 0.8802 (pt) cc_final: 0.8597 (pt) REVERT: E 32 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8813 (mt-10) REVERT: E 77 TYR cc_start: 0.8553 (m-80) cc_final: 0.8353 (m-10) REVERT: E 90 PHE cc_start: 0.8693 (t80) cc_final: 0.8074 (t80) REVERT: E 106 LEU cc_start: 0.9340 (mt) cc_final: 0.9098 (mt) REVERT: E 110 PHE cc_start: 0.8985 (m-80) cc_final: 0.8666 (m-80) REVERT: E 113 MET cc_start: 0.9179 (mtp) cc_final: 0.8683 (mtp) REVERT: E 134 GLU cc_start: 0.8975 (tt0) cc_final: 0.8648 (tm-30) REVERT: E 135 PHE cc_start: 0.8461 (m-10) cc_final: 0.7801 (m-80) REVERT: E 196 MET cc_start: 0.8231 (mmm) cc_final: 0.7701 (mmm) REVERT: E 220 MET cc_start: 0.8888 (mmm) cc_final: 0.8392 (mmm) REVERT: E 221 TRP cc_start: 0.7792 (t60) cc_final: 0.7092 (t60) REVERT: E 260 PHE cc_start: 0.8758 (m-80) cc_final: 0.8519 (m-10) REVERT: F 118 LYS cc_start: 0.7428 (pttm) cc_final: 0.7226 (ptpp) REVERT: F 139 TRP cc_start: 0.8655 (m-90) cc_final: 0.8349 (m-90) REVERT: F 141 ILE cc_start: 0.8837 (mt) cc_final: 0.8626 (mm) REVERT: F 168 LEU cc_start: 0.9367 (mt) cc_final: 0.9128 (mt) REVERT: F 169 ASN cc_start: 0.8483 (m-40) cc_final: 0.7720 (t0) REVERT: G 224 LEU cc_start: 0.8590 (mt) cc_final: 0.7264 (mt) REVERT: G 256 VAL cc_start: 0.9413 (t) cc_final: 0.9184 (p) REVERT: H 218 MET cc_start: 0.8328 (tpt) cc_final: 0.7985 (tpp) REVERT: H 242 TYR cc_start: 0.7420 (p90) cc_final: 0.7186 (p90) REVERT: H 258 ASP cc_start: 0.9369 (p0) cc_final: 0.8995 (p0) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2147 time to fit residues: 68.3505 Evaluate side-chains 151 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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: 4.9990 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 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 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN F 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11970 Z= 0.216 Angle : 0.582 6.960 16624 Z= 0.326 Chirality : 0.042 0.144 1790 Planarity : 0.005 0.102 1856 Dihedral : 22.818 139.013 2160 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.25), residues: 1202 helix: 1.03 (0.26), residues: 422 sheet: 0.31 (0.47), residues: 128 loop : -0.51 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 208 HIS 0.006 0.001 HIS F 79 PHE 0.028 0.002 PHE B 189 TYR 0.031 0.002 TYR F 127 ARG 0.005 0.000 ARG G 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 205 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9327 (mm) cc_final: 0.9088 (tp) REVERT: A 25 ILE cc_start: 0.8780 (pt) cc_final: 0.8562 (pt) REVERT: A 28 GLU cc_start: 0.8545 (mp0) cc_final: 0.8166 (tm-30) REVERT: A 72 PHE cc_start: 0.7250 (m-80) cc_final: 0.6810 (m-80) REVERT: A 77 TYR cc_start: 0.7907 (m-10) cc_final: 0.7555 (m-10) REVERT: A 90 PHE cc_start: 0.8647 (t80) cc_final: 0.7879 (t80) REVERT: A 113 MET cc_start: 0.9229 (mtp) cc_final: 0.8857 (mtp) REVERT: A 196 MET cc_start: 0.8453 (mmm) cc_final: 0.7904 (mmm) REVERT: A 220 MET cc_start: 0.9059 (tpp) cc_final: 0.8401 (mmm) REVERT: A 221 TRP cc_start: 0.7617 (t60) cc_final: 0.7282 (t60) REVERT: B 97 GLU cc_start: 0.8566 (pm20) cc_final: 0.8247 (mm-30) REVERT: B 141 ILE cc_start: 0.8964 (mt) cc_final: 0.8734 (mm) REVERT: B 168 LEU cc_start: 0.9383 (mt) cc_final: 0.9141 (mt) REVERT: B 169 ASN cc_start: 0.8704 (m-40) cc_final: 0.8141 (t0) REVERT: C 256 VAL cc_start: 0.9332 (t) cc_final: 0.9024 (p) REVERT: D 245 VAL cc_start: 0.9165 (m) cc_final: 0.8607 (p) REVERT: E 14 GLN cc_start: 0.7124 (tp40) cc_final: 0.6792 (tp40) REVERT: E 25 ILE cc_start: 0.8810 (pt) cc_final: 0.8594 (pt) REVERT: E 29 GLN cc_start: 0.9228 (mt0) cc_final: 0.8634 (mm-40) REVERT: E 72 PHE cc_start: 0.7666 (m-80) cc_final: 0.7232 (m-80) REVERT: E 77 TYR cc_start: 0.8625 (m-80) cc_final: 0.8330 (m-10) REVERT: E 90 PHE cc_start: 0.8660 (t80) cc_final: 0.7955 (t80) REVERT: E 106 LEU cc_start: 0.9350 (mt) cc_final: 0.9065 (mt) REVERT: E 110 PHE cc_start: 0.9010 (m-80) cc_final: 0.8388 (m-80) REVERT: E 113 MET cc_start: 0.9105 (mtp) cc_final: 0.8659 (mtp) REVERT: E 134 GLU cc_start: 0.8993 (tt0) cc_final: 0.8584 (tm-30) REVERT: E 135 PHE cc_start: 0.8467 (m-10) cc_final: 0.8079 (m-80) REVERT: E 196 MET cc_start: 0.8550 (mmm) cc_final: 0.8049 (mmm) REVERT: E 220 MET cc_start: 0.8866 (mmm) cc_final: 0.8328 (mmm) REVERT: E 221 TRP cc_start: 0.7909 (t60) cc_final: 0.7200 (t60) REVERT: F 110 PHE cc_start: 0.8637 (m-10) cc_final: 0.8390 (m-10) REVERT: F 118 LYS cc_start: 0.7620 (pttm) cc_final: 0.7396 (ptpp) REVERT: F 141 ILE cc_start: 0.8860 (mt) cc_final: 0.8630 (mm) REVERT: F 168 LEU cc_start: 0.9402 (mt) cc_final: 0.9154 (mt) REVERT: F 169 ASN cc_start: 0.8513 (m-40) cc_final: 0.7785 (t0) REVERT: G 256 VAL cc_start: 0.9444 (t) cc_final: 0.9213 (p) REVERT: H 218 MET cc_start: 0.8613 (tpt) cc_final: 0.8218 (tpp) REVERT: H 258 ASP cc_start: 0.9403 (p0) cc_final: 0.9010 (p0) REVERT: H 259 ARG cc_start: 0.8665 (ptm160) cc_final: 0.8457 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2053 time to fit residues: 62.4538 Evaluate side-chains 146 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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: 0.4980 chunk 104 optimal weight: 7.9990 chunk 111 optimal weight: 0.0010 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 52 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6336 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= 0.168 Angle : 0.571 7.085 16624 Z= 0.316 Chirality : 0.042 0.157 1790 Planarity : 0.005 0.090 1856 Dihedral : 22.620 137.716 2160 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.19 % Allowed : 0.58 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.21 (0.25), residues: 1202 helix: 1.10 (0.26), residues: 424 sheet: 0.16 (0.44), residues: 140 loop : -0.48 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 208 HIS 0.005 0.001 HIS B 79 PHE 0.025 0.001 PHE B 189 TYR 0.016 0.001 TYR E 85 ARG 0.003 0.000 ARG F 94 *********************** 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 217 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 215 time to evaluate : 1.314 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 19 LEU cc_start: 0.9288 (mm) cc_final: 0.9063 (tp) REVERT: A 25 ILE cc_start: 0.8692 (pt) cc_final: 0.8429 (pt) REVERT: A 28 GLU cc_start: 0.8641 (mp0) cc_final: 0.8302 (tm-30) REVERT: A 72 PHE cc_start: 0.7323 (m-80) cc_final: 0.6892 (m-80) REVERT: A 77 TYR cc_start: 0.7887 (m-10) cc_final: 0.7514 (m-10) REVERT: A 90 PHE cc_start: 0.8531 (t80) cc_final: 0.7794 (t80) REVERT: A 113 MET cc_start: 0.9224 (mtp) cc_final: 0.8847 (mtp) REVERT: A 196 MET cc_start: 0.8339 (mmm) cc_final: 0.7854 (mmm) REVERT: A 220 MET cc_start: 0.9068 (tpp) cc_final: 0.8417 (mmm) REVERT: A 221 TRP cc_start: 0.7604 (t60) cc_final: 0.7302 (t60) REVERT: B 97 GLU cc_start: 0.8464 (pm20) cc_final: 0.8223 (mm-30) REVERT: B 110 PHE cc_start: 0.8429 (m-10) cc_final: 0.7969 (m-10) REVERT: B 141 ILE cc_start: 0.8880 (mt) cc_final: 0.8673 (mm) REVERT: B 168 LEU cc_start: 0.9377 (mt) cc_final: 0.9117 (mt) REVERT: B 169 ASN cc_start: 0.8663 (m-40) cc_final: 0.8006 (t0) REVERT: C 218 MET cc_start: 0.8724 (mpp) cc_final: 0.8356 (mpp) REVERT: C 224 LEU cc_start: 0.8613 (mp) cc_final: 0.7738 (mp) REVERT: C 256 VAL cc_start: 0.9291 (t) cc_final: 0.8913 (p) REVERT: D 245 VAL cc_start: 0.9195 (m) cc_final: 0.8619 (p) REVERT: E 29 GLN cc_start: 0.9235 (mt0) cc_final: 0.8712 (mm-40) REVERT: E 56 LEU cc_start: 0.9271 (mm) cc_final: 0.8521 (tp) REVERT: E 72 PHE cc_start: 0.7547 (m-80) cc_final: 0.7082 (m-80) REVERT: E 77 TYR cc_start: 0.8597 (m-80) cc_final: 0.8288 (m-10) REVERT: E 90 PHE cc_start: 0.8628 (t80) cc_final: 0.8051 (t80) REVERT: E 106 LEU cc_start: 0.9386 (mt) cc_final: 0.9141 (mt) REVERT: E 110 PHE cc_start: 0.8914 (m-10) cc_final: 0.8566 (m-80) REVERT: E 113 MET cc_start: 0.9120 (mtp) cc_final: 0.8631 (mtp) REVERT: E 134 GLU cc_start: 0.8985 (tt0) cc_final: 0.8600 (tm-30) REVERT: E 135 PHE cc_start: 0.8322 (m-10) cc_final: 0.7901 (m-10) REVERT: E 196 MET cc_start: 0.8346 (mmm) cc_final: 0.7965 (mmm) REVERT: E 220 MET cc_start: 0.8911 (mmm) cc_final: 0.8365 (mmm) REVERT: E 221 TRP cc_start: 0.7794 (t60) cc_final: 0.7042 (t60) REVERT: F 64 MET cc_start: 0.7300 (ppp) cc_final: 0.6962 (ppp) REVERT: F 110 PHE cc_start: 0.8648 (m-10) cc_final: 0.8410 (m-10) REVERT: F 141 ILE cc_start: 0.8721 (mt) cc_final: 0.8520 (mm) REVERT: F 168 LEU cc_start: 0.9349 (mt) cc_final: 0.9085 (mt) REVERT: F 169 ASN cc_start: 0.8444 (m-40) cc_final: 0.7682 (t0) REVERT: G 256 VAL cc_start: 0.9416 (t) cc_final: 0.9149 (p) REVERT: G 258 ASP cc_start: 0.7989 (p0) cc_final: 0.7620 (m-30) REVERT: H 218 MET cc_start: 0.8512 (tpt) cc_final: 0.8121 (tpp) REVERT: H 242 TYR cc_start: 0.7590 (p90) cc_final: 0.7347 (p90) REVERT: H 258 ASP cc_start: 0.9388 (p0) cc_final: 0.9009 (p0) outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 0.1982 time to fit residues: 63.9188 Evaluate side-chains 157 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 0.0170 chunk 98 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 0.0670 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** A 167 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 52 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.6560 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= 0.161 Angle : 0.567 7.663 16624 Z= 0.312 Chirality : 0.042 0.151 1790 Planarity : 0.005 0.082 1856 Dihedral : 22.576 136.618 2160 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.19 % Allowed : 0.10 % 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: 0.19 (0.25), residues: 1202 helix: 1.11 (0.26), residues: 424 sheet: -0.13 (0.39), residues: 182 loop : -0.44 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 208 HIS 0.007 0.001 HIS E 9 PHE 0.033 0.001 PHE F 135 TYR 0.020 0.001 TYR E 85 ARG 0.004 0.000 ARG E 20 ********************** 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: 2 poor density : 215 time to evaluate : 1.199 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 28 GLU cc_start: 0.8500 (mp0) cc_final: 0.8136 (tm-30) REVERT: A 72 PHE cc_start: 0.7227 (m-80) cc_final: 0.6949 (m-80) REVERT: A 77 TYR cc_start: 0.7844 (m-10) cc_final: 0.7454 (m-10) REVERT: A 90 PHE cc_start: 0.8351 (t80) cc_final: 0.7857 (t80) REVERT: A 113 MET cc_start: 0.9251 (mtp) cc_final: 0.8802 (mtp) REVERT: A 196 MET cc_start: 0.8437 (mmm) cc_final: 0.7985 (mmm) REVERT: A 220 MET cc_start: 0.9038 (tpp) cc_final: 0.8331 (mmm) REVERT: A 221 TRP cc_start: 0.7553 (t60) cc_final: 0.7247 (t60) REVERT: B 97 GLU cc_start: 0.8433 (pm20) cc_final: 0.8202 (mm-30) REVERT: B 168 LEU cc_start: 0.9363 (mt) cc_final: 0.9135 (mt) REVERT: B 169 ASN cc_start: 0.8656 (m-40) cc_final: 0.8014 (t0) REVERT: C 218 MET cc_start: 0.8605 (mpp) cc_final: 0.8323 (mpp) REVERT: C 224 LEU cc_start: 0.8661 (mp) cc_final: 0.7798 (mp) REVERT: C 256 VAL cc_start: 0.9316 (t) cc_final: 0.8827 (p) REVERT: C 261 ILE cc_start: 0.9351 (mm) cc_final: 0.9105 (mm) REVERT: D 224 LEU cc_start: 0.9260 (pp) cc_final: 0.9054 (tt) REVERT: D 245 VAL cc_start: 0.9197 (m) cc_final: 0.8753 (p) REVERT: E 56 LEU cc_start: 0.9266 (mm) cc_final: 0.8502 (tp) REVERT: E 72 PHE cc_start: 0.7396 (m-80) cc_final: 0.6963 (m-80) REVERT: E 77 TYR cc_start: 0.8575 (m-80) cc_final: 0.8305 (m-10) REVERT: E 90 PHE cc_start: 0.8646 (t80) cc_final: 0.8175 (t80) REVERT: E 106 LEU cc_start: 0.9375 (mt) cc_final: 0.9122 (mt) REVERT: E 110 PHE cc_start: 0.8808 (m-10) cc_final: 0.8453 (m-80) REVERT: E 113 MET cc_start: 0.9085 (mtp) cc_final: 0.8572 (mtp) REVERT: E 134 GLU cc_start: 0.8875 (tt0) cc_final: 0.8521 (tm-30) REVERT: E 135 PHE cc_start: 0.8327 (m-10) cc_final: 0.7873 (m-10) REVERT: E 196 MET cc_start: 0.8364 (mmm) cc_final: 0.7987 (mmm) REVERT: E 220 MET cc_start: 0.8902 (mmm) cc_final: 0.8277 (mmm) REVERT: E 221 TRP cc_start: 0.7775 (t60) cc_final: 0.7030 (t60) REVERT: F 168 LEU cc_start: 0.9336 (mt) cc_final: 0.9059 (mt) REVERT: F 169 ASN cc_start: 0.8357 (m-40) cc_final: 0.7472 (t0) REVERT: G 218 MET cc_start: 0.8725 (mpp) cc_final: 0.8357 (mpp) REVERT: G 224 LEU cc_start: 0.8827 (mp) cc_final: 0.7436 (mm) REVERT: G 256 VAL cc_start: 0.9350 (t) cc_final: 0.8881 (p) REVERT: H 258 ASP cc_start: 0.9378 (p0) cc_final: 0.9053 (p0) outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 0.2078 time to fit residues: 65.8326 Evaluate side-chains 154 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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: 0.0050 chunk 30 optimal weight: 0.0050 chunk 90 optimal weight: 0.6980 chunk 14 optimal weight: 0.0010 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN B 79 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.075287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.063654 restraints weight = 58724.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.065488 restraints weight = 35316.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.066772 restraints weight = 23874.456| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11970 Z= 0.158 Angle : 0.570 8.232 16624 Z= 0.316 Chirality : 0.042 0.178 1790 Planarity : 0.005 0.076 1856 Dihedral : 22.547 136.286 2160 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % 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: 0.14 (0.26), residues: 1202 helix: 1.01 (0.26), residues: 426 sheet: -0.26 (0.37), residues: 202 loop : -0.38 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 208 HIS 0.005 0.001 HIS E 9 PHE 0.028 0.001 PHE F 135 TYR 0.019 0.001 TYR E 85 ARG 0.003 0.000 ARG F 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2480.61 seconds wall clock time: 45 minutes 33.40 seconds (2733.40 seconds total)