Starting phenix.real_space_refine on Thu Feb 15 03:55:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgs_27428/02_2024/8dgs_27428_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgs_27428/02_2024/8dgs_27428.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgs_27428/02_2024/8dgs_27428_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgs_27428/02_2024/8dgs_27428_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgs_27428/02_2024/8dgs_27428_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgs_27428/02_2024/8dgs_27428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgs_27428/02_2024/8dgs_27428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgs_27428/02_2024/8dgs_27428_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgs_27428/02_2024/8dgs_27428_updated.pdb" } resolution = 4.3 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= 0.003 sd= 0.045 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: 9 Type Number sf(0) Gaussians I 1 10.91 5 Zn 2 6.06 5 P 11 5.49 5 Mg 2 5.21 5 S 66 5.16 5 C 6995 2.51 5 N 1905 2.21 5 O 2106 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11089 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3424 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2465 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 314, 2459 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 314, 2459 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2498 Chain: "C" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1846 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 5, 'TRANS': 223} Chain: "D" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1833 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 223} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1398 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1324 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 167, 1324 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1257 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' ZN': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'AGS': 1, 'LCJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 733 SG CYS A 248 53.497 61.150 43.069 1.00 85.78 S ATOM 758 SG CYS A 251 56.058 63.787 42.201 1.00107.33 S ATOM 940 SG CYS A 272 57.047 60.027 41.972 1.00121.87 S ATOM 846 SG CYS A 261 43.870 52.039 42.561 1.00106.38 S ATOM 868 SG CYS A 264 43.355 53.941 45.755 1.00115.33 S ATOM 998 SG CYS A 280 43.643 50.219 46.131 1.00172.39 S Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N MET E 1 " occ=0.76 ... (3 atoms not shown) pdb=" CB MET E 1 " occ=0.76 residue: pdb=" N MET E 67 " occ=0.94 ... (6 atoms not shown) pdb=" CE MET E 67 " occ=0.94 residue: pdb=" N GLN E 70 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN E 70 " occ=0.97 residue: pdb=" N TYR E 71 " occ=0.84 ... (10 atoms not shown) pdb=" OH TYR E 71 " occ=0.84 residue: pdb=" N AGLN E 99 " occ=0.58 ... (16 atoms not shown) pdb=" NE2BGLN E 99 " occ=0.42 residue: pdb=" N GLU E 107 " occ=0.82 ... (7 atoms not shown) pdb=" OE2 GLU E 107 " occ=0.82 residue: pdb=" N GLN E 150 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN E 150 " occ=0.97 Time building chain proxies: 8.00, per 1000 atoms: 0.72 Number of scatterers: 11089 At special positions: 0 Unit cell: (83.3, 115.6, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) I 1 52.95 Zn 2 29.99 S 66 16.00 P 11 15.00 Mg 2 11.99 F 1 9.00 O 2106 8.00 N 1905 7.00 C 6995 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.87 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" ND1 HIS A 269 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 251 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 248 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 272 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" ND1 HIS A 235 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 261 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 264 " pdb="ZN ZN A 803 " - pdb=" SG CYS A 280 " Number of angles added : 6 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 7 sheets defined 52.1% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 177 through 187 removed outlier: 4.622A pdb=" N LYS A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.655A pdb=" N SER A 273 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 506 Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 550 through 569 removed outlier: 3.542A pdb=" N MET A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 566 " --> pdb=" O GLN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 635 through 651 Processing helix chain 'A' and resid 662 through 670 Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 721 through 724 No H-bonds generated for 'chain 'A' and resid 721 through 724' Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.622A pdb=" N GLN B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N HIS B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 163 through 183 removed outlier: 3.567A pdb=" N LYS B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 213 through 221 removed outlier: 4.184A pdb=" N ASN B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 241 through 258 removed outlier: 3.680A pdb=" N SER B 244 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 No H-bonds generated for 'chain 'B' and resid 269 through 272' Processing helix chain 'B' and resid 310 through 319 Processing helix chain 'B' and resid 332 through 341 Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.626A pdb=" N GLN C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 38 through 69 removed outlier: 3.735A pdb=" N ASN C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 104 Processing helix chain 'C' and resid 112 through 130 Processing helix chain 'C' and resid 136 through 159 Processing helix chain 'C' and resid 165 through 181 Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 212 through 229 Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 20 through 32 Processing helix chain 'D' and resid 38 through 68 removed outlier: 3.567A pdb=" N LEU D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 103 removed outlier: 3.633A pdb=" N ASP D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 132 removed outlier: 4.034A pdb=" N VAL D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 159 Processing helix chain 'D' and resid 165 through 180 Processing helix chain 'D' and resid 185 through 201 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 213 through 229 Processing helix chain 'E' and resid 16 through 25 Processing helix chain 'E' and resid 62 through 74 removed outlier: 4.983A pdb=" N ALA E 66 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 104 removed outlier: 4.668A pdb=" N HIS E 94 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 137 Processing helix chain 'E' and resid 152 through 166 Processing sheet with id= A, first strand: chain 'A' and resid 165 through 170 removed outlier: 4.783A pdb=" N VAL A 197 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 241 removed outlier: 3.769A pdb=" N LYS A 240 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 258 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 469 through 475 Processing sheet with id= D, first strand: chain 'A' and resid 582 through 585 Processing sheet with id= E, first strand: chain 'B' and resid 129 through 135 removed outlier: 6.521A pdb=" N CYS B 142 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA B 132 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER B 140 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR B 134 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 92 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 86 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS B 70 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 196 through 198 Processing sheet with id= G, first strand: chain 'E' and resid 140 through 143 removed outlier: 3.581A pdb=" N THR E 2 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY E 10 " --> pdb=" O THR E 58 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1595 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 5.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 3718 1.37 - 1.55: 7464 1.55 - 1.74: 20 1.74 - 1.92: 103 1.92 - 2.11: 3 Bond restraints: 11308 Sorted by residual: bond pdb=" O2P SEP A 729 " pdb=" P SEP A 729 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O3P SEP A 729 " pdb=" P SEP A 729 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" O1P SEP A 729 " pdb=" P SEP A 729 " ideal model delta sigma weight residual 1.610 1.512 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" N3B GNP E 202 " pdb=" PG GNP E 202 " ideal model delta sigma weight residual 1.801 1.711 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" O5' GNP E 202 " pdb=" PA GNP E 202 " ideal model delta sigma weight residual 1.660 1.586 0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 11303 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.45: 321 106.45 - 113.34: 6231 113.34 - 120.23: 4031 120.23 - 127.12: 4601 127.12 - 134.01: 117 Bond angle restraints: 15301 Sorted by residual: angle pdb=" CB GLN E 150 " pdb=" CG GLN E 150 " pdb=" CD GLN E 150 " ideal model delta sigma weight residual 112.60 123.32 -10.72 1.70e+00 3.46e-01 3.98e+01 angle pdb=" C HIS A 235 " pdb=" N ASN A 236 " pdb=" CA ASN A 236 " ideal model delta sigma weight residual 122.41 115.09 7.32 1.47e+00 4.63e-01 2.48e+01 angle pdb=" CA HIS A 235 " pdb=" CB HIS A 235 " pdb=" CG HIS A 235 " ideal model delta sigma weight residual 113.80 118.41 -4.61 1.00e+00 1.00e+00 2.12e+01 angle pdb=" CA HIS A 235 " pdb=" C HIS A 235 " pdb=" O HIS A 235 " ideal model delta sigma weight residual 121.58 116.81 4.77 1.16e+00 7.43e-01 1.69e+01 angle pdb=" N VAL C 132 " pdb=" CA VAL C 132 " pdb=" C VAL C 132 " ideal model delta sigma weight residual 113.42 108.88 4.54 1.17e+00 7.31e-01 1.51e+01 ... (remaining 15296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 6486 16.69 - 33.39: 346 33.39 - 50.08: 94 50.08 - 66.77: 29 66.77 - 83.46: 6 Dihedral angle restraints: 6961 sinusoidal: 2910 harmonic: 4051 Sorted by residual: dihedral pdb=" C HIS A 235 " pdb=" N HIS A 235 " pdb=" CA HIS A 235 " pdb=" CB HIS A 235 " ideal model delta harmonic sigma weight residual -122.60 -112.74 -9.86 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" CA THR E 35 " pdb=" C THR E 35 " pdb=" N ILE E 36 " pdb=" CA ILE E 36 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA THR E 144 " pdb=" C THR E 144 " pdb=" N SER E 145 " pdb=" CA SER E 145 " ideal model delta harmonic sigma weight residual 180.00 162.91 17.09 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 6958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1511 0.075 - 0.151: 169 0.151 - 0.226: 14 0.226 - 0.302: 2 0.302 - 0.377: 1 Chirality restraints: 1697 Sorted by residual: chirality pdb=" CA HIS A 235 " pdb=" N HIS A 235 " pdb=" C HIS A 235 " pdb=" CB HIS A 235 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA CYS E 51 " pdb=" N CYS E 51 " pdb=" C CYS E 51 " pdb=" CB CYS E 51 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ARG E 149 " pdb=" N ARG E 149 " pdb=" C ARG E 149 " pdb=" CB ARG E 149 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1694 not shown) Planarity restraints: 1952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 78 " -0.026 2.00e-02 2.50e+03 1.60e-02 4.51e+00 pdb=" CG PHE E 78 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE E 78 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE E 78 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE E 78 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE E 78 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE E 78 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 707 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO A 708 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 708 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 708 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 235 " 0.019 2.00e-02 2.50e+03 1.57e-02 3.72e+00 pdb=" CG HIS A 235 " -0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS A 235 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS A 235 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 235 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS A 235 " 0.001 2.00e-02 2.50e+03 ... (remaining 1949 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.56: 136 2.56 - 3.16: 9583 3.16 - 3.76: 18470 3.76 - 4.36: 25160 4.36 - 4.96: 40424 Nonbonded interactions: 93773 Sorted by model distance: nonbonded pdb=" OD1 ASN A 163 " pdb=" NH1 ARG E 41 " model vdw 1.957 2.520 nonbonded pdb=" O3B AGS B 801 " pdb="MG MG B 802 " model vdw 1.978 2.170 nonbonded pdb=" O2A AGS B 801 " pdb="MG MG B 802 " model vdw 1.996 2.170 nonbonded pdb="MG MG E 201 " pdb=" O2G GNP E 202 " model vdw 2.027 2.170 nonbonded pdb="MG MG E 201 " pdb=" O2B GNP E 202 " model vdw 2.031 2.170 ... (remaining 93768 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 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 59 or (resid 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 through 201 or (resid \ 202 and (name N or name CA or name C or name O or name CB )) or resid 203 throug \ h 230)) selection = chain 'D' } 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=0.16 max=1.00 mean=0.99 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: 1.190 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: 6.060 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 37.350 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 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 : 0.004 0.101 11308 Z= 0.297 Angle : 0.644 10.896 15301 Z= 0.367 Chirality : 0.048 0.377 1697 Planarity : 0.003 0.049 1952 Dihedral : 11.849 83.463 4349 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.73 % Allowed : 6.64 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 1.74 (0.23), residues: 1360 helix: 2.41 (0.19), residues: 729 sheet: 0.09 (0.44), residues: 140 loop : -0.45 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 531 HIS 0.010 0.001 HIS A 235 PHE 0.026 0.002 PHE E 78 TYR 0.024 0.002 TYR E 96 ARG 0.005 0.000 ARG E 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 320 time to evaluate : 1.407 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: A 195 CYS cc_start: 0.4824 (m) cc_final: 0.3453 (m) REVERT: A 249 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7817 (t0) REVERT: A 255 LEU cc_start: 0.9085 (tp) cc_final: 0.8665 (tp) REVERT: A 517 MET cc_start: 0.8415 (mmm) cc_final: 0.8027 (mmm) REVERT: A 594 ASP cc_start: 0.8171 (t0) cc_final: 0.7777 (t0) REVERT: A 604 TRP cc_start: 0.8383 (m-10) cc_final: 0.8146 (m-10) REVERT: A 695 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7891 (tt0) REVERT: B 115 LEU cc_start: 0.9782 (mt) cc_final: 0.9517 (pp) REVERT: B 157 LYS cc_start: 0.9559 (mttt) cc_final: 0.9310 (ptpp) REVERT: B 187 MET cc_start: 0.5602 (OUTLIER) cc_final: 0.4999 (ptm) REVERT: B 188 HIS cc_start: 0.5122 (t-90) cc_final: 0.4289 (t-170) REVERT: B 342 LEU cc_start: 0.8843 (mt) cc_final: 0.8551 (mt) REVERT: C 68 LYS cc_start: 0.9536 (OUTLIER) cc_final: 0.9323 (tptp) REVERT: C 93 ILE cc_start: 0.9672 (mt) cc_final: 0.9414 (pt) REVERT: C 150 GLN cc_start: 0.9526 (mm-40) cc_final: 0.9035 (mm-40) REVERT: C 190 GLN cc_start: 0.9338 (tt0) cc_final: 0.8999 (mt0) REVERT: C 207 ASN cc_start: 0.9524 (OUTLIER) cc_final: 0.9158 (p0) REVERT: C 215 THR cc_start: 0.9181 (t) cc_final: 0.8968 (p) REVERT: C 220 LEU cc_start: 0.9748 (mt) cc_final: 0.9525 (mt) REVERT: D 15 GLN cc_start: 0.9300 (mm-40) cc_final: 0.9090 (mm-40) REVERT: D 22 MET cc_start: 0.8917 (ttp) cc_final: 0.8700 (ttp) REVERT: D 50 ASN cc_start: 0.9280 (m110) cc_final: 0.8978 (m-40) REVERT: D 62 ILE cc_start: 0.9496 (mm) cc_final: 0.9287 (tt) REVERT: D 94 CYS cc_start: 0.9175 (m) cc_final: 0.8913 (p) REVERT: D 95 TYR cc_start: 0.8903 (m-10) cc_final: 0.8457 (m-10) REVERT: D 100 LEU cc_start: 0.9386 (tt) cc_final: 0.8947 (mt) REVERT: D 121 MET cc_start: 0.9541 (mtp) cc_final: 0.9096 (mmm) REVERT: D 147 LYS cc_start: 0.9640 (mttt) cc_final: 0.9023 (tppt) REVERT: D 150 GLN cc_start: 0.9133 (mt0) cc_final: 0.8903 (mm-40) REVERT: D 178 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.9001 (m-10) REVERT: D 218 MET cc_start: 0.8968 (mtm) cc_final: 0.8736 (mtm) REVERT: D 221 LEU cc_start: 0.9748 (mt) cc_final: 0.9490 (mt) REVERT: D 222 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7891 (ttp-170) outliers start: 42 outliers final: 12 residues processed: 348 average time/residue: 0.2705 time to fit residues: 125.9114 Evaluate side-chains 202 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 185 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN D 224 ASN E 70 GLN E 99 GLN A Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11308 Z= 0.226 Angle : 0.597 6.943 15301 Z= 0.312 Chirality : 0.043 0.151 1697 Planarity : 0.004 0.044 1952 Dihedral : 6.102 57.186 1597 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.58 % Allowed : 2.57 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 1.43 (0.23), residues: 1360 helix: 1.88 (0.19), residues: 726 sheet: 0.30 (0.47), residues: 122 loop : -0.17 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 247 HIS 0.007 0.001 HIS B 145 PHE 0.039 0.002 PHE B 334 TYR 0.040 0.002 TYR E 157 ARG 0.006 0.001 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ASP cc_start: 0.8394 (m-30) cc_final: 0.8118 (t70) REVERT: A 255 LEU cc_start: 0.9113 (tp) cc_final: 0.8615 (tp) REVERT: A 555 ASP cc_start: 0.9103 (t0) cc_final: 0.8835 (t0) REVERT: A 594 ASP cc_start: 0.8359 (t0) cc_final: 0.7654 (t0) REVERT: A 695 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8006 (tt0) REVERT: A 698 LYS cc_start: 0.8788 (mmtp) cc_final: 0.8353 (mmtt) REVERT: B 146 MET cc_start: 0.8512 (mmm) cc_final: 0.8036 (mmt) REVERT: B 345 ASN cc_start: 0.8863 (t0) cc_final: 0.8489 (t0) REVERT: C 77 GLN cc_start: 0.9331 (mp10) cc_final: 0.9119 (mp10) REVERT: C 190 GLN cc_start: 0.9209 (tt0) cc_final: 0.8929 (mt0) REVERT: C 202 GLU cc_start: 0.8553 (mp0) cc_final: 0.8344 (mp0) REVERT: D 14 GLU cc_start: 0.9555 (tm-30) cc_final: 0.9309 (tm-30) REVERT: D 50 ASN cc_start: 0.9323 (m110) cc_final: 0.8988 (m-40) REVERT: D 95 TYR cc_start: 0.8948 (m-10) cc_final: 0.8687 (m-10) REVERT: D 100 LEU cc_start: 0.9318 (tt) cc_final: 0.8790 (mt) REVERT: D 121 MET cc_start: 0.9541 (mtp) cc_final: 0.9038 (mmm) REVERT: D 147 LYS cc_start: 0.9608 (mttt) cc_final: 0.9139 (tppt) REVERT: D 149 TYR cc_start: 0.8921 (m-10) cc_final: 0.8588 (m-80) REVERT: D 160 MET cc_start: 0.9043 (tmm) cc_final: 0.8813 (tmm) REVERT: D 218 MET cc_start: 0.9047 (mtm) cc_final: 0.8826 (mtm) REVERT: D 219 GLN cc_start: 0.8739 (tp40) cc_final: 0.8512 (tm-30) REVERT: E 55 ILE cc_start: 0.5388 (mm) cc_final: 0.4660 (mm) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.2391 time to fit residues: 74.7745 Evaluate side-chains 148 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 130 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 41 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11308 Z= 0.175 Angle : 0.557 13.280 15301 Z= 0.290 Chirality : 0.041 0.158 1697 Planarity : 0.004 0.043 1952 Dihedral : 5.892 55.398 1597 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.50 % Allowed : 3.15 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 1.51 (0.24), residues: 1360 helix: 1.92 (0.19), residues: 724 sheet: 0.36 (0.44), residues: 129 loop : -0.09 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 604 HIS 0.007 0.001 HIS C 104 PHE 0.048 0.002 PHE E 156 TYR 0.035 0.001 TYR E 157 ARG 0.004 0.000 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ASP cc_start: 0.8456 (m-30) cc_final: 0.8071 (t70) REVERT: A 268 PHE cc_start: 0.8696 (p90) cc_final: 0.8488 (p90) REVERT: A 555 ASP cc_start: 0.9037 (t0) cc_final: 0.8731 (t0) REVERT: A 695 GLU cc_start: 0.8743 (mt-10) cc_final: 0.7834 (tt0) REVERT: B 115 LEU cc_start: 0.9794 (mt) cc_final: 0.9576 (pp) REVERT: B 143 MET cc_start: 0.9195 (ptp) cc_final: 0.8859 (mpp) REVERT: B 146 MET cc_start: 0.8849 (mmm) cc_final: 0.8290 (mmt) REVERT: B 312 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8780 (mt-10) REVERT: B 315 ASP cc_start: 0.9083 (t0) cc_final: 0.8555 (p0) REVERT: B 316 TYR cc_start: 0.9140 (t80) cc_final: 0.8934 (t80) REVERT: B 345 ASN cc_start: 0.8831 (t0) cc_final: 0.8462 (t0) REVERT: C 14 GLU cc_start: 0.9252 (pp20) cc_final: 0.8891 (pp20) REVERT: C 22 MET cc_start: 0.8799 (ttm) cc_final: 0.8462 (ttp) REVERT: C 26 MET cc_start: 0.9641 (mmp) cc_final: 0.9336 (tpp) REVERT: C 202 GLU cc_start: 0.8557 (mp0) cc_final: 0.8356 (mp0) REVERT: C 218 MET cc_start: 0.9464 (ptp) cc_final: 0.8908 (ttt) REVERT: C 220 LEU cc_start: 0.9782 (mt) cc_final: 0.9581 (mt) REVERT: C 221 LEU cc_start: 0.9778 (mt) cc_final: 0.9557 (mt) REVERT: D 14 GLU cc_start: 0.9507 (tm-30) cc_final: 0.9239 (tm-30) REVERT: D 26 MET cc_start: 0.9320 (mmm) cc_final: 0.8971 (mmm) REVERT: D 50 ASN cc_start: 0.9327 (m110) cc_final: 0.9081 (m-40) REVERT: D 95 TYR cc_start: 0.9008 (m-10) cc_final: 0.8716 (m-10) REVERT: D 100 LEU cc_start: 0.9272 (tt) cc_final: 0.8687 (mt) REVERT: D 121 MET cc_start: 0.9545 (mtp) cc_final: 0.9027 (mmm) REVERT: D 147 LYS cc_start: 0.9634 (mttt) cc_final: 0.9119 (tppt) REVERT: D 174 PHE cc_start: 0.8872 (t80) cc_final: 0.8667 (t80) REVERT: D 218 MET cc_start: 0.9061 (mtm) cc_final: 0.8771 (mtm) REVERT: D 219 GLN cc_start: 0.8719 (tp40) cc_final: 0.8389 (tm-30) REVERT: E 55 ILE cc_start: 0.5394 (mm) cc_final: 0.5021 (mm) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2229 time to fit residues: 63.5815 Evaluate side-chains 152 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 128 optimal weight: 50.0000 chunk 63 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11308 Z= 0.223 Angle : 0.566 7.182 15301 Z= 0.294 Chirality : 0.042 0.194 1697 Planarity : 0.004 0.039 1952 Dihedral : 5.917 55.639 1597 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.50 % Allowed : 2.99 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 1.34 (0.23), residues: 1360 helix: 1.79 (0.19), residues: 723 sheet: 0.33 (0.45), residues: 130 loop : -0.20 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 604 HIS 0.006 0.001 HIS C 104 PHE 0.018 0.002 PHE B 334 TYR 0.030 0.002 TYR E 157 ARG 0.004 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 CYS cc_start: 0.4463 (m) cc_final: 0.3878 (m) REVERT: A 210 TRP cc_start: 0.4238 (m100) cc_final: 0.3382 (m100) REVERT: A 268 PHE cc_start: 0.8647 (p90) cc_final: 0.8434 (p90) REVERT: A 555 ASP cc_start: 0.8963 (t0) cc_final: 0.8663 (t0) REVERT: A 689 MET cc_start: 0.8101 (ttm) cc_final: 0.7825 (ttm) REVERT: B 143 MET cc_start: 0.9218 (ptp) cc_final: 0.8848 (mpp) REVERT: B 308 MET cc_start: 0.8533 (tpt) cc_final: 0.8143 (tpp) REVERT: B 312 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8677 (mt-10) REVERT: B 345 ASN cc_start: 0.8809 (t0) cc_final: 0.8466 (t0) REVERT: C 14 GLU cc_start: 0.9185 (pp20) cc_final: 0.8922 (pp20) REVERT: C 22 MET cc_start: 0.8816 (ttm) cc_final: 0.8445 (ttp) REVERT: C 202 GLU cc_start: 0.8573 (mp0) cc_final: 0.8370 (mp0) REVERT: C 221 LEU cc_start: 0.9778 (mt) cc_final: 0.9567 (mt) REVERT: D 14 GLU cc_start: 0.9538 (tm-30) cc_final: 0.9288 (tm-30) REVERT: D 26 MET cc_start: 0.9345 (mmm) cc_final: 0.8996 (mmm) REVERT: D 50 ASN cc_start: 0.9361 (m110) cc_final: 0.9135 (m-40) REVERT: D 93 ILE cc_start: 0.9614 (pt) cc_final: 0.9322 (pt) REVERT: D 95 TYR cc_start: 0.9000 (m-10) cc_final: 0.8735 (m-10) REVERT: D 100 LEU cc_start: 0.9315 (tt) cc_final: 0.8758 (mt) REVERT: D 121 MET cc_start: 0.9580 (mtp) cc_final: 0.9018 (mmm) REVERT: D 147 LYS cc_start: 0.9639 (mttt) cc_final: 0.9124 (tppt) REVERT: D 160 MET cc_start: 0.8952 (tmm) cc_final: 0.8752 (tmm) REVERT: D 174 PHE cc_start: 0.8889 (t80) cc_final: 0.8672 (t80) REVERT: D 218 MET cc_start: 0.9058 (mtm) cc_final: 0.8804 (mtm) REVERT: D 219 GLN cc_start: 0.8750 (tp40) cc_final: 0.8492 (tm-30) REVERT: E 55 ILE cc_start: 0.5472 (mm) cc_final: 0.4707 (mm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2169 time to fit residues: 58.8070 Evaluate side-chains 148 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 65 optimal weight: 0.0670 chunk 115 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11308 Z= 0.251 Angle : 0.586 7.975 15301 Z= 0.311 Chirality : 0.041 0.191 1697 Planarity : 0.004 0.037 1952 Dihedral : 5.976 54.559 1597 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.50 % Allowed : 1.66 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 1.13 (0.23), residues: 1360 helix: 1.62 (0.19), residues: 722 sheet: -0.08 (0.45), residues: 124 loop : -0.20 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 604 HIS 0.006 0.001 HIS A 269 PHE 0.027 0.002 PHE C 174 TYR 0.026 0.002 TYR E 157 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 CYS cc_start: 0.4466 (m) cc_final: 0.4183 (m) REVERT: A 210 TRP cc_start: 0.4281 (m100) cc_final: 0.3444 (m100) REVERT: A 255 LEU cc_start: 0.8996 (tp) cc_final: 0.8446 (tp) REVERT: A 555 ASP cc_start: 0.9013 (t0) cc_final: 0.8714 (t0) REVERT: A 594 ASP cc_start: 0.8788 (m-30) cc_final: 0.8395 (m-30) REVERT: A 689 MET cc_start: 0.7973 (ttm) cc_final: 0.7734 (ttm) REVERT: B 143 MET cc_start: 0.9126 (ptp) cc_final: 0.8763 (mpp) REVERT: B 146 MET cc_start: 0.8972 (mmm) cc_final: 0.8309 (mmt) REVERT: B 308 MET cc_start: 0.8514 (tpt) cc_final: 0.8106 (tpp) REVERT: B 312 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8651 (mt-10) REVERT: B 345 ASN cc_start: 0.8772 (t0) cc_final: 0.8454 (t0) REVERT: C 9 ARG cc_start: 0.9296 (tpt90) cc_final: 0.9055 (tpp-160) REVERT: C 22 MET cc_start: 0.8850 (ttm) cc_final: 0.8496 (ttp) REVERT: C 121 MET cc_start: 0.9097 (mtp) cc_final: 0.8887 (mtp) REVERT: C 202 GLU cc_start: 0.8607 (mp0) cc_final: 0.8389 (mp0) REVERT: C 221 LEU cc_start: 0.9760 (mt) cc_final: 0.9545 (mt) REVERT: D 14 GLU cc_start: 0.9529 (tm-30) cc_final: 0.9239 (tm-30) REVERT: D 26 MET cc_start: 0.9345 (mmm) cc_final: 0.8934 (mmm) REVERT: D 93 ILE cc_start: 0.9615 (pt) cc_final: 0.9289 (pt) REVERT: D 95 TYR cc_start: 0.9045 (m-10) cc_final: 0.8673 (m-10) REVERT: D 100 LEU cc_start: 0.9340 (tt) cc_final: 0.8766 (mt) REVERT: D 121 MET cc_start: 0.9597 (mtp) cc_final: 0.9013 (mmm) REVERT: D 147 LYS cc_start: 0.9628 (mttt) cc_final: 0.9148 (tppt) REVERT: D 174 PHE cc_start: 0.8860 (t80) cc_final: 0.8646 (t80) REVERT: D 218 MET cc_start: 0.9073 (mtm) cc_final: 0.8803 (mtm) REVERT: D 219 GLN cc_start: 0.8706 (tp40) cc_final: 0.8170 (tp40) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2250 time to fit residues: 58.7353 Evaluate side-chains 138 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN D 50 ASN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 11308 Z= 0.424 Angle : 0.772 14.630 15301 Z= 0.402 Chirality : 0.045 0.230 1697 Planarity : 0.005 0.073 1952 Dihedral : 6.601 59.724 1597 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.50 % Allowed : 2.41 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 0.36 (0.22), residues: 1360 helix: 0.89 (0.18), residues: 714 sheet: -0.07 (0.43), residues: 132 loop : -0.47 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 604 HIS 0.013 0.003 HIS A 585 PHE 0.021 0.003 PHE A 583 TYR 0.031 0.003 TYR C 82 ARG 0.007 0.001 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 CYS cc_start: 0.4740 (m) cc_final: 0.4058 (m) REVERT: A 210 TRP cc_start: 0.4506 (m100) cc_final: 0.3636 (m100) REVERT: A 255 LEU cc_start: 0.9051 (tp) cc_final: 0.8657 (tp) REVERT: A 268 PHE cc_start: 0.8735 (p90) cc_final: 0.8534 (p90) REVERT: A 555 ASP cc_start: 0.9020 (t0) cc_final: 0.8770 (t0) REVERT: A 594 ASP cc_start: 0.8824 (m-30) cc_final: 0.8534 (m-30) REVERT: A 617 ILE cc_start: 0.9327 (pt) cc_final: 0.9094 (pt) REVERT: A 620 MET cc_start: 0.8280 (mtt) cc_final: 0.7942 (mtp) REVERT: B 143 MET cc_start: 0.9142 (ptp) cc_final: 0.8783 (mpp) REVERT: B 146 MET cc_start: 0.9076 (mmm) cc_final: 0.8479 (mmt) REVERT: B 345 ASN cc_start: 0.8776 (t0) cc_final: 0.8496 (t0) REVERT: C 9 ARG cc_start: 0.9267 (tpt90) cc_final: 0.9024 (tpp-160) REVERT: C 22 MET cc_start: 0.8978 (ttm) cc_final: 0.8684 (ttp) REVERT: C 121 MET cc_start: 0.9134 (mtp) cc_final: 0.8837 (mtp) REVERT: D 14 GLU cc_start: 0.9569 (tm-30) cc_final: 0.9287 (tm-30) REVERT: D 95 TYR cc_start: 0.8898 (m-10) cc_final: 0.8574 (m-10) REVERT: D 121 MET cc_start: 0.9649 (mtp) cc_final: 0.9038 (mmm) REVERT: D 147 LYS cc_start: 0.9634 (mttt) cc_final: 0.9188 (tppt) REVERT: D 150 GLN cc_start: 0.9136 (mt0) cc_final: 0.8725 (tp-100) REVERT: D 153 PHE cc_start: 0.9381 (t80) cc_final: 0.8911 (t80) REVERT: D 160 MET cc_start: 0.9033 (tmm) cc_final: 0.8782 (tmm) REVERT: D 218 MET cc_start: 0.9160 (mtm) cc_final: 0.8937 (mtm) REVERT: D 219 GLN cc_start: 0.8746 (tp40) cc_final: 0.8238 (tp40) REVERT: D 221 LEU cc_start: 0.9663 (mt) cc_final: 0.9461 (mt) REVERT: E 55 ILE cc_start: 0.5531 (mm) cc_final: 0.4876 (mm) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2149 time to fit residues: 51.2590 Evaluate side-chains 133 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11308 Z= 0.250 Angle : 0.602 7.845 15301 Z= 0.320 Chirality : 0.042 0.163 1697 Planarity : 0.004 0.053 1952 Dihedral : 6.181 51.173 1597 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.50 % Allowed : 1.58 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 0.70 (0.23), residues: 1360 helix: 1.30 (0.19), residues: 713 sheet: -0.20 (0.42), residues: 132 loop : -0.45 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 604 HIS 0.009 0.001 HIS C 104 PHE 0.018 0.002 PHE D 177 TYR 0.025 0.002 TYR E 157 ARG 0.007 0.000 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.392 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 187 MET cc_start: 0.7858 (mmp) cc_final: 0.7174 (mmt) REVERT: A 195 CYS cc_start: 0.4890 (m) cc_final: 0.4266 (m) REVERT: A 210 TRP cc_start: 0.4629 (m100) cc_final: 0.3831 (m100) REVERT: A 255 LEU cc_start: 0.9007 (tp) cc_final: 0.8567 (tp) REVERT: A 555 ASP cc_start: 0.8991 (t0) cc_final: 0.8718 (t0) REVERT: A 594 ASP cc_start: 0.8757 (m-30) cc_final: 0.8421 (m-30) REVERT: A 617 ILE cc_start: 0.9277 (pt) cc_final: 0.9051 (pt) REVERT: A 620 MET cc_start: 0.8287 (mtt) cc_final: 0.7940 (mtp) REVERT: A 713 SER cc_start: 0.9170 (m) cc_final: 0.8945 (m) REVERT: B 94 MET cc_start: 0.8554 (mtp) cc_final: 0.8041 (mtp) REVERT: B 143 MET cc_start: 0.9142 (ptp) cc_final: 0.8780 (mpp) REVERT: B 345 ASN cc_start: 0.8777 (t0) cc_final: 0.8571 (t0) REVERT: C 22 MET cc_start: 0.8918 (ttm) cc_final: 0.8540 (ttp) REVERT: C 121 MET cc_start: 0.9101 (mtp) cc_final: 0.8798 (mtp) REVERT: C 202 GLU cc_start: 0.8658 (mp0) cc_final: 0.8407 (mp0) REVERT: C 220 LEU cc_start: 0.9821 (mt) cc_final: 0.9615 (mt) REVERT: D 14 GLU cc_start: 0.9544 (tm-30) cc_final: 0.9281 (tm-30) REVERT: D 95 TYR cc_start: 0.8844 (m-10) cc_final: 0.8540 (m-10) REVERT: D 100 LEU cc_start: 0.9342 (tt) cc_final: 0.8779 (mt) REVERT: D 121 MET cc_start: 0.9618 (mtp) cc_final: 0.9023 (mmm) REVERT: D 147 LYS cc_start: 0.9614 (mttt) cc_final: 0.9191 (tppt) REVERT: D 150 GLN cc_start: 0.9134 (mt0) cc_final: 0.8701 (tp-100) REVERT: D 160 MET cc_start: 0.9033 (tmm) cc_final: 0.8757 (tmm) REVERT: D 217 ILE cc_start: 0.9530 (mm) cc_final: 0.8942 (tp) REVERT: D 218 MET cc_start: 0.9114 (mtm) cc_final: 0.8851 (mtm) REVERT: D 219 GLN cc_start: 0.8753 (tp40) cc_final: 0.8163 (tp-100) REVERT: D 221 LEU cc_start: 0.9665 (mt) cc_final: 0.9454 (mt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2263 time to fit residues: 57.1392 Evaluate side-chains 137 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN D 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11308 Z= 0.164 Angle : 0.564 8.192 15301 Z= 0.298 Chirality : 0.041 0.157 1697 Planarity : 0.004 0.043 1952 Dihedral : 6.157 55.516 1597 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.58 % Allowed : 1.00 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 1.02 (0.23), residues: 1360 helix: 1.64 (0.19), residues: 710 sheet: -0.14 (0.42), residues: 134 loop : -0.40 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 604 HIS 0.008 0.001 HIS C 104 PHE 0.026 0.002 PHE C 174 TYR 0.023 0.002 TYR E 157 ARG 0.007 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.195 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 254 LEU cc_start: 0.9484 (tp) cc_final: 0.9186 (tt) REVERT: A 255 LEU cc_start: 0.8996 (tp) cc_final: 0.8608 (tp) REVERT: A 555 ASP cc_start: 0.8946 (t0) cc_final: 0.8689 (t0) REVERT: A 565 ASP cc_start: 0.8383 (t70) cc_final: 0.7956 (t70) REVERT: A 594 ASP cc_start: 0.8656 (m-30) cc_final: 0.8395 (m-30) REVERT: A 640 TYR cc_start: 0.9294 (t80) cc_final: 0.9018 (t80) REVERT: A 713 SER cc_start: 0.9095 (m) cc_final: 0.8888 (m) REVERT: B 94 MET cc_start: 0.8584 (mtp) cc_final: 0.8087 (mtp) REVERT: B 146 MET cc_start: 0.8996 (mmm) cc_final: 0.8287 (mmt) REVERT: B 230 MET cc_start: 0.7840 (tpp) cc_final: 0.6704 (tmm) REVERT: B 308 MET cc_start: 0.8122 (tpt) cc_final: 0.7658 (tpt) REVERT: B 312 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8700 (mt-10) REVERT: B 341 CYS cc_start: 0.8172 (p) cc_final: 0.7890 (p) REVERT: C 14 GLU cc_start: 0.9059 (pp20) cc_final: 0.8771 (pp20) REVERT: C 22 MET cc_start: 0.8864 (ttm) cc_final: 0.8447 (ttp) REVERT: C 121 MET cc_start: 0.9074 (mtp) cc_final: 0.8813 (mtp) REVERT: C 202 GLU cc_start: 0.8646 (mp0) cc_final: 0.8405 (mp0) REVERT: D 14 GLU cc_start: 0.9506 (tm-30) cc_final: 0.9143 (tm-30) REVERT: D 95 TYR cc_start: 0.8856 (m-10) cc_final: 0.8579 (m-10) REVERT: D 100 LEU cc_start: 0.9330 (tt) cc_final: 0.8765 (mt) REVERT: D 121 MET cc_start: 0.9583 (mtp) cc_final: 0.8982 (mmm) REVERT: D 147 LYS cc_start: 0.9611 (mttt) cc_final: 0.9132 (tppt) REVERT: D 150 GLN cc_start: 0.9193 (mt0) cc_final: 0.8642 (tp-100) REVERT: D 160 MET cc_start: 0.9022 (tmm) cc_final: 0.8731 (tmm) REVERT: D 217 ILE cc_start: 0.9495 (mm) cc_final: 0.8874 (tp) REVERT: D 218 MET cc_start: 0.9026 (mtm) cc_final: 0.8780 (mtm) REVERT: D 219 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8182 (tp-100) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2209 time to fit residues: 57.0358 Evaluate side-chains 145 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 126 optimal weight: 30.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11308 Z= 0.193 Angle : 0.592 8.525 15301 Z= 0.307 Chirality : 0.042 0.161 1697 Planarity : 0.004 0.036 1952 Dihedral : 6.028 53.205 1597 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.58 % Allowed : 0.58 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 0.98 (0.23), residues: 1360 helix: 1.61 (0.19), residues: 714 sheet: -0.17 (0.42), residues: 134 loop : -0.42 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 604 HIS 0.007 0.001 HIS C 104 PHE 0.030 0.002 PHE C 174 TYR 0.021 0.002 TYR E 157 ARG 0.004 0.000 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 CYS cc_start: 0.4906 (m) cc_final: 0.4417 (m) REVERT: A 210 TRP cc_start: 0.4603 (m100) cc_final: 0.3708 (m100) REVERT: A 254 LEU cc_start: 0.9486 (tp) cc_final: 0.9177 (tt) REVERT: A 255 LEU cc_start: 0.9002 (tp) cc_final: 0.8558 (tp) REVERT: A 554 ILE cc_start: 0.9015 (mm) cc_final: 0.8770 (tp) REVERT: A 555 ASP cc_start: 0.8941 (t0) cc_final: 0.8715 (t0) REVERT: A 565 ASP cc_start: 0.8335 (t70) cc_final: 0.7931 (t70) REVERT: A 640 TYR cc_start: 0.9307 (t80) cc_final: 0.9088 (t80) REVERT: A 689 MET cc_start: 0.7830 (ttm) cc_final: 0.7568 (ttm) REVERT: B 94 MET cc_start: 0.8535 (mtp) cc_final: 0.8055 (mtp) REVERT: B 230 MET cc_start: 0.7886 (tpp) cc_final: 0.6758 (tmm) REVERT: B 308 MET cc_start: 0.8100 (tpt) cc_final: 0.7856 (tpt) REVERT: C 14 GLU cc_start: 0.9035 (pp20) cc_final: 0.8765 (pp20) REVERT: C 22 MET cc_start: 0.8868 (ttm) cc_final: 0.8462 (ttp) REVERT: C 121 MET cc_start: 0.9070 (mtp) cc_final: 0.8810 (mtp) REVERT: C 202 GLU cc_start: 0.8646 (mp0) cc_final: 0.8417 (mp0) REVERT: C 223 ASP cc_start: 0.9328 (m-30) cc_final: 0.8997 (m-30) REVERT: D 14 GLU cc_start: 0.9505 (tm-30) cc_final: 0.9170 (tm-30) REVERT: D 26 MET cc_start: 0.9306 (mmm) cc_final: 0.8974 (mmm) REVERT: D 95 TYR cc_start: 0.8858 (m-10) cc_final: 0.8589 (m-10) REVERT: D 100 LEU cc_start: 0.9358 (tt) cc_final: 0.8797 (mt) REVERT: D 121 MET cc_start: 0.9598 (mtp) cc_final: 0.8984 (mmm) REVERT: D 147 LYS cc_start: 0.9605 (mttt) cc_final: 0.9119 (tppt) REVERT: D 150 GLN cc_start: 0.9201 (mt0) cc_final: 0.8732 (tp-100) REVERT: D 217 ILE cc_start: 0.9504 (mm) cc_final: 0.8887 (tp) REVERT: D 218 MET cc_start: 0.9026 (mtm) cc_final: 0.8797 (mtm) REVERT: D 219 GLN cc_start: 0.8717 (tp-100) cc_final: 0.7864 (tp-100) REVERT: D 221 LEU cc_start: 0.9663 (mt) cc_final: 0.9459 (mt) REVERT: D 223 ASP cc_start: 0.9198 (m-30) cc_final: 0.8544 (m-30) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2076 time to fit residues: 53.3663 Evaluate side-chains 140 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11308 Z= 0.354 Angle : 0.729 13.084 15301 Z= 0.379 Chirality : 0.044 0.217 1697 Planarity : 0.005 0.038 1952 Dihedral : 6.220 51.086 1597 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.58 % Allowed : 0.75 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 0.37 (0.23), residues: 1360 helix: 1.03 (0.19), residues: 715 sheet: -0.38 (0.42), residues: 130 loop : -0.59 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 604 HIS 0.009 0.002 HIS C 104 PHE 0.027 0.002 PHE E 156 TYR 0.053 0.002 TYR E 157 ARG 0.005 0.001 ARG A 671 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 LEU cc_start: 0.9068 (tp) cc_final: 0.8638 (tp) REVERT: A 555 ASP cc_start: 0.9005 (t0) cc_final: 0.8712 (t0) REVERT: A 565 ASP cc_start: 0.8401 (t70) cc_final: 0.7958 (t70) REVERT: A 610 PHE cc_start: 0.8046 (m-10) cc_final: 0.7324 (m-10) REVERT: A 617 ILE cc_start: 0.9282 (pt) cc_final: 0.8621 (pt) REVERT: A 620 MET cc_start: 0.8342 (mtt) cc_final: 0.7917 (mtt) REVERT: A 689 MET cc_start: 0.7553 (ttm) cc_final: 0.7327 (ttm) REVERT: B 94 MET cc_start: 0.8392 (mtp) cc_final: 0.7898 (mtp) REVERT: B 308 MET cc_start: 0.8038 (tpt) cc_final: 0.7811 (tpt) REVERT: C 14 GLU cc_start: 0.9033 (pp20) cc_final: 0.8832 (pp20) REVERT: C 22 MET cc_start: 0.8990 (ttm) cc_final: 0.8601 (ttp) REVERT: C 50 ASN cc_start: 0.9494 (m-40) cc_final: 0.9163 (t0) REVERT: C 121 MET cc_start: 0.9125 (mtp) cc_final: 0.8824 (mtp) REVERT: C 202 GLU cc_start: 0.8735 (mp0) cc_final: 0.8452 (mp0) REVERT: C 223 ASP cc_start: 0.9357 (m-30) cc_final: 0.9034 (m-30) REVERT: D 14 GLU cc_start: 0.9515 (tm-30) cc_final: 0.9305 (tm-30) REVERT: D 26 MET cc_start: 0.9378 (mmm) cc_final: 0.9033 (mmm) REVERT: D 95 TYR cc_start: 0.8867 (m-10) cc_final: 0.8530 (m-10) REVERT: D 100 LEU cc_start: 0.9393 (tt) cc_final: 0.8859 (mt) REVERT: D 121 MET cc_start: 0.9658 (mtp) cc_final: 0.9028 (mmm) REVERT: D 147 LYS cc_start: 0.9612 (mttt) cc_final: 0.9170 (tppt) REVERT: D 150 GLN cc_start: 0.9290 (mt0) cc_final: 0.8821 (tp-100) REVERT: D 153 PHE cc_start: 0.9390 (t80) cc_final: 0.9184 (t80) REVERT: D 218 MET cc_start: 0.9122 (mtm) cc_final: 0.8865 (mtm) REVERT: D 219 GLN cc_start: 0.8837 (tp-100) cc_final: 0.8040 (tp-100) REVERT: D 221 LEU cc_start: 0.9645 (mt) cc_final: 0.9404 (mt) REVERT: D 223 ASP cc_start: 0.9233 (m-30) cc_final: 0.8692 (m-30) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1984 time to fit residues: 49.1863 Evaluate side-chains 128 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 105 optimal weight: 0.0030 chunk 44 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 13 optimal weight: 0.0270 chunk 19 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 overall best weight: 1.9852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.078038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.046736 restraints weight = 199089.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.050048 restraints weight = 56884.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.052167 restraints weight = 29227.683| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11308 Z= 0.205 Angle : 0.614 8.910 15301 Z= 0.324 Chirality : 0.043 0.179 1697 Planarity : 0.004 0.036 1952 Dihedral : 5.951 50.276 1597 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.58 % Allowed : 0.41 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % 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: 0.67 (0.23), residues: 1360 helix: 1.39 (0.19), residues: 709 sheet: -0.31 (0.42), residues: 130 loop : -0.61 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP A 604 HIS 0.009 0.001 HIS B 100 PHE 0.028 0.002 PHE D 174 TYR 0.036 0.002 TYR D 178 ARG 0.003 0.000 ARG D 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2295.60 seconds wall clock time: 43 minutes 31.10 seconds (2611.10 seconds total)