Starting phenix.real_space_refine on Fri Mar 15 02:50:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/03_2024/6bx3_7303.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/03_2024/6bx3_7303.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/03_2024/6bx3_7303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/03_2024/6bx3_7303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/03_2024/6bx3_7303.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/03_2024/6bx3_7303.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= 0.001 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 6608 2.51 5 N 1786 2.21 5 O 2015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 973": "NH1" <-> "NH2" Residue "E ARG 983": "NH1" <-> "NH2" Residue "F PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 328": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "A PHE 92": "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: 10456 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1432 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "K" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1520 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 3 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 70 Chain: "M" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 328 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 36} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1526 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 168 Chain: "B" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3050 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 16, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2296 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 11, 'TRANS': 302} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 76 Time building chain proxies: 5.88, per 1000 atoms: 0.56 Number of scatterers: 10456 At special positions: 0 Unit cell: (137, 109, 155, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 2015 8.00 N 1786 7.00 C 6608 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: 3.92 Conformation dependent library (CDL) restraints added in 1.8 seconds 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2658 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 15 sheets defined 19.6% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'E' and resid 799 through 824 removed outlier: 4.384A pdb=" N ARG E 805 " --> pdb=" O TRP E 801 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER E 814 " --> pdb=" O GLU E 810 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP E 815 " --> pdb=" O GLU E 811 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN E 817 " --> pdb=" O ALA E 813 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE E 818 " --> pdb=" O SER E 814 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 824 " --> pdb=" O LEU E 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 933 Processing helix chain 'E' and resid 974 through 988 removed outlier: 3.570A pdb=" N ASN E 987 " --> pdb=" O ARG E 983 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 106 removed outlier: 3.659A pdb=" N LEU K 101 " --> pdb=" O SER K 98 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER K 102 " --> pdb=" O GLU K 99 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE K 103 " --> pdb=" O GLY K 100 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N SER K 104 " --> pdb=" O LEU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 200 Processing helix chain 'K' and resid 459 through 463 removed outlier: 3.704A pdb=" N GLN K 462 " --> pdb=" O TYR K 459 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 500 removed outlier: 3.747A pdb=" N LYS K 483 " --> pdb=" O ASP K 479 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 144 Processing helix chain 'M' and resid 152 through 162 removed outlier: 3.523A pdb=" N LEU M 157 " --> pdb=" O LEU M 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 129 Processing helix chain 'N' and resid 130 through 142 removed outlier: 4.278A pdb=" N LEU N 134 " --> pdb=" O VAL N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 159 removed outlier: 3.726A pdb=" N TYR N 156 " --> pdb=" O VAL N 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 Processing helix chain 'F' and resid 135 through 145 removed outlier: 3.574A pdb=" N GLU F 143 " --> pdb=" O LYS F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 158 removed outlier: 3.858A pdb=" N PHE F 154 " --> pdb=" O LYS F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 171 removed outlier: 3.653A pdb=" N ASP F 169 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 4.713A pdb=" N GLU F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU F 200 " --> pdb=" O GLN F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 208 Processing helix chain 'F' and resid 208 through 241 removed outlier: 4.844A pdb=" N LEU F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASP F 218 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP F 228 " --> pdb=" O MET F 224 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP F 230 " --> pdb=" O LYS F 226 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL F 235 " --> pdb=" O ALA F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 283 Processing helix chain 'F' and resid 311 through 349 removed outlier: 3.698A pdb=" N TYR F 315 " --> pdb=" O ASN F 311 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU F 349 " --> pdb=" O TYR F 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 1023 through 1026 removed outlier: 6.424A pdb=" N THR E1024 " --> pdb=" O TYR E1039 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E1037 " --> pdb=" O LYS E1026 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 137 through 139 Processing sheet with id=AA3, first strand: chain 'K' and resid 204 through 205 Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 23 removed outlier: 4.321A pdb=" N ASP B 317 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 34 removed outlier: 5.318A pdb=" N CYS B 31 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 44 " --> pdb=" O CYS B 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.683A pdb=" N LEU B 98 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 109 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 122 removed outlier: 4.097A pdb=" N TYR B 141 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 176 removed outlier: 5.456A pdb=" N CYS B 174 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY B 187 " --> pdb=" O CYS B 174 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 193 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER B 209 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE B 195 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 269 through 274 removed outlier: 6.431A pdb=" N SER B 285 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE B 272 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL B 283 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE B 274 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N TYR B 281 " --> pdb=" O PHE B 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 61 through 62 removed outlier: 4.263A pdb=" N ALA A 71 " --> pdb=" O CYS A 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 102 through 104 removed outlier: 3.947A pdb=" N THR A 103 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 112 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS A 121 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 120 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR A 133 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE A 122 " --> pdb=" O MET A 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 131 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AB4, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AB5, first strand: chain 'A' and resid 204 through 207 removed outlier: 3.686A pdb=" N LEU A 204 " --> pdb=" O TRP A 216 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 206 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 213 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR A 226 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A 215 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 248 through 250 223 hydrogen bonds defined for protein. 627 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: 2.93 Time building geometry restraints manager: 4.29 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: 2172 1.33 - 1.45: 2588 1.45 - 1.58: 5836 1.58 - 1.70: 0 1.70 - 1.83: 62 Bond restraints: 10658 Sorted by residual: bond pdb=" CA HIS A 90 " pdb=" CB HIS A 90 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.35e-02 5.49e+03 4.00e+01 bond pdb=" C THR N 131 " pdb=" N PRO N 132 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.20e-02 6.94e+03 1.76e+01 bond pdb=" C ALA E 943 " pdb=" O ALA E 943 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.24e-02 6.50e+03 7.42e+00 bond pdb=" CB TRP A 312 " pdb=" CG TRP A 312 " ideal model delta sigma weight residual 1.498 1.415 0.083 3.10e-02 1.04e+03 7.11e+00 bond pdb=" N SER K 102 " pdb=" CA SER K 102 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.20e-02 6.94e+03 6.89e+00 ... (remaining 10653 not shown) Histogram of bond angle deviations from ideal: 94.40 - 102.69: 43 102.69 - 110.99: 3831 110.99 - 119.29: 5021 119.29 - 127.59: 5479 127.59 - 135.89: 145 Bond angle restraints: 14519 Sorted by residual: angle pdb=" N ILE E 972 " pdb=" CA ILE E 972 " pdb=" C ILE E 972 " ideal model delta sigma weight residual 110.72 124.94 -14.22 1.01e+00 9.80e-01 1.98e+02 angle pdb=" N ALA B 350 " pdb=" CA ALA B 350 " pdb=" C ALA B 350 " ideal model delta sigma weight residual 111.07 123.29 -12.22 1.07e+00 8.73e-01 1.30e+02 angle pdb=" C ASN B 25 " pdb=" N PRO B 26 " pdb=" CA PRO B 26 " ideal model delta sigma weight residual 119.05 131.02 -11.97 1.11e+00 8.12e-01 1.16e+02 angle pdb=" N GLU B 356 " pdb=" CA GLU B 356 " pdb=" C GLU B 356 " ideal model delta sigma weight residual 109.59 94.40 15.19 1.47e+00 4.63e-01 1.07e+02 angle pdb=" C LYS B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta sigma weight residual 119.87 129.81 -9.94 1.04e+00 9.25e-01 9.13e+01 ... (remaining 14514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 5702 14.94 - 29.87: 484 29.87 - 44.81: 97 44.81 - 59.74: 19 59.74 - 74.68: 11 Dihedral angle restraints: 6313 sinusoidal: 2210 harmonic: 4103 Sorted by residual: dihedral pdb=" CA HIS A 286 " pdb=" C HIS A 286 " pdb=" N SER A 287 " pdb=" CA SER A 287 " ideal model delta harmonic sigma weight residual 180.00 -120.35 -59.65 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA ASN B 66 " pdb=" C ASN B 66 " pdb=" N MET B 67 " pdb=" CA MET B 67 " ideal model delta harmonic sigma weight residual -180.00 -125.42 -54.58 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA ILE E 947 " pdb=" C ILE E 947 " pdb=" N HIS E 948 " pdb=" CA HIS E 948 " ideal model delta harmonic sigma weight residual 180.00 -127.07 -52.93 0 5.00e+00 4.00e-02 1.12e+02 ... (remaining 6310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1420 0.098 - 0.196: 218 0.196 - 0.294: 33 0.294 - 0.392: 12 0.392 - 0.490: 3 Chirality restraints: 1686 Sorted by residual: chirality pdb=" CB THR K 439 " pdb=" CA THR K 439 " pdb=" OG1 THR K 439 " pdb=" CG2 THR K 439 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CG LEU B 154 " pdb=" CB LEU B 154 " pdb=" CD1 LEU B 154 " pdb=" CD2 LEU B 154 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA PRO B 26 " pdb=" N PRO B 26 " pdb=" C PRO B 26 " pdb=" CB PRO B 26 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.84e+00 ... (remaining 1683 not shown) Planarity restraints: 1879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 164 " -0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C ILE F 164 " 0.077 2.00e-02 2.50e+03 pdb=" O ILE F 164 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL F 165 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 113 " 0.020 2.00e-02 2.50e+03 4.07e-02 1.65e+01 pdb=" C PHE B 113 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE B 113 " 0.027 2.00e-02 2.50e+03 pdb=" N ASP B 114 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 943 " -0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ALA E 943 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA E 943 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG E 944 " -0.020 2.00e-02 2.50e+03 ... (remaining 1876 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.86: 3 1.86 - 2.62: 230 2.62 - 3.38: 14421 3.38 - 4.14: 24674 4.14 - 4.90: 41121 Nonbonded interactions: 80449 Sorted by model distance: nonbonded pdb=" CB ASP K 125 " pdb=" OH TYR K 482 " model vdw 1.094 3.440 nonbonded pdb=" O CYS F 263 " pdb=" OG1 THR F 297 " model vdw 1.520 2.440 nonbonded pdb=" CB ASP K 125 " pdb=" CZ TYR K 482 " model vdw 1.775 3.660 nonbonded pdb=" O ASP K 96 " pdb=" CB ARG K 123 " model vdw 1.917 3.440 nonbonded pdb=" CG2 THR F 297 " pdb=" CE1 HIS F 304 " model vdw 1.955 3.680 ... (remaining 80444 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 'M' and (resid 122 through 138 or (resid 139 through 140 and (name N or n \ ame CA or name C or name O or name CB )) or resid 141 through 146 or (resid 147 \ and (name N or name CA or name C or name O or name CB )) or resid 148 through 16 \ 1)) selection = (chain 'N' and (resid 122 through 125 or (resid 126 and (name N or name CA or na \ me C or name O or name CB )) or resid 127 through 142 or (resid 143 and (name N \ or name CA or name C or name O or name CB )) or resid 144 through 161)) } 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=0.07 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.890 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 29.380 Find NCS groups from input model: 0.350 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.007 0.085 10658 Z= 0.499 Angle : 1.492 15.194 14519 Z= 0.898 Chirality : 0.079 0.490 1686 Planarity : 0.008 0.072 1879 Dihedral : 12.650 74.679 3655 Min Nonbonded Distance : 1.094 Molprobity Statistics. All-atom Clashscore : 24.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 18.77 % Favored : 81.16 % Rotamer: Outliers : 0.97 % Allowed : 9.17 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 1.26 % 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: -5.00 (0.17), residues: 1385 helix: -2.80 (0.24), residues: 229 sheet: -2.94 (0.34), residues: 173 loop : -3.83 (0.15), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP K 135 HIS 0.015 0.003 HIS A 286 PHE 0.030 0.004 PHE F 283 TYR 0.031 0.004 TYR K 202 ARG 0.009 0.001 ARG E 841 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 283 time to evaluate : 1.311 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: E 819 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9165 (mm-30) REVERT: E 934 ASN cc_start: 0.9318 (t160) cc_final: 0.8889 (p0) REVERT: E 975 PRO cc_start: 0.8494 (Cg_exo) cc_final: 0.8142 (Cg_endo) REVERT: E 979 MET cc_start: 0.8978 (tpt) cc_final: 0.8650 (tpp) REVERT: E 998 ASP cc_start: 0.7816 (m-30) cc_final: 0.6241 (p0) REVERT: E 1026 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8197 (mtmm) REVERT: E 1039 TYR cc_start: 0.8089 (t80) cc_final: 0.7490 (t80) REVERT: K 194 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8301 (tm-30) REVERT: K 199 PHE cc_start: 0.9470 (t80) cc_final: 0.8996 (t80) REVERT: K 469 VAL cc_start: 0.6236 (t) cc_final: 0.5743 (t) REVERT: K 483 LYS cc_start: 0.9018 (mptt) cc_final: 0.8808 (mmtt) REVERT: M 139 ARG cc_start: 0.8745 (mmp-170) cc_final: 0.7931 (mtt180) REVERT: M 147 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7057 (mp0) REVERT: N 123 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7781 (mtt180) REVERT: F 120 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8239 (mm-30) REVERT: F 204 LYS cc_start: 0.9089 (ttpm) cc_final: 0.8748 (ptpp) REVERT: F 223 GLU cc_start: 0.9661 (tt0) cc_final: 0.9441 (tm-30) REVERT: F 228 ASP cc_start: 0.8918 (m-30) cc_final: 0.8712 (t0) REVERT: F 291 LYS cc_start: 0.8185 (pttp) cc_final: 0.7087 (mmmt) REVERT: B 54 ASP cc_start: 0.8339 (p0) cc_final: 0.7381 (p0) REVERT: B 59 ARG cc_start: 0.8741 (mtt-85) cc_final: 0.8394 (mmm-85) REVERT: B 67 MET cc_start: 0.9076 (mpm) cc_final: 0.8741 (mmm) REVERT: B 144 ASP cc_start: 0.9572 (m-30) cc_final: 0.9095 (t70) REVERT: B 258 HIS cc_start: 0.7965 (t-90) cc_final: 0.7657 (t-170) REVERT: B 268 GLN cc_start: 0.8249 (pp30) cc_final: 0.8009 (pp30) REVERT: B 319 ASN cc_start: 0.9046 (t0) cc_final: 0.8768 (t0) REVERT: B 320 TRP cc_start: 0.8524 (m100) cc_final: 0.8259 (m100) REVERT: B 354 ASP cc_start: 0.8753 (m-30) cc_final: 0.7945 (t0) REVERT: A 116 MET cc_start: 0.7837 (tmt) cc_final: 0.7478 (tmm) REVERT: A 127 ASN cc_start: 0.9137 (t160) cc_final: 0.8848 (t0) REVERT: A 149 ASN cc_start: 0.9139 (m-40) cc_final: 0.8871 (m-40) REVERT: A 196 LYS cc_start: 0.8564 (tttp) cc_final: 0.8238 (ttmm) REVERT: A 249 GLU cc_start: 0.7906 (mp0) cc_final: 0.7594 (mp0) REVERT: A 291 MET cc_start: 0.8426 (tpp) cc_final: 0.7926 (mmm) outliers start: 10 outliers final: 3 residues processed: 291 average time/residue: 0.2410 time to fit residues: 95.5418 Evaluate side-chains 176 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.5980 chunk 105 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 215 HIS ** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN B 225 ASN B 330 ASN ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10658 Z= 0.263 Angle : 0.836 13.431 14519 Z= 0.439 Chirality : 0.051 0.397 1686 Planarity : 0.005 0.046 1879 Dihedral : 8.654 49.938 1491 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.26 % Favored : 82.74 % Rotamer: Outliers : 0.39 % Allowed : 4.63 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.74 % 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: -4.33 (0.19), residues: 1385 helix: -1.76 (0.28), residues: 254 sheet: -2.92 (0.36), residues: 161 loop : -3.45 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 135 HIS 0.009 0.002 HIS F 304 PHE 0.020 0.002 PHE B 355 TYR 0.024 0.002 TYR M 156 ARG 0.004 0.000 ARG E 804 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 237 time to evaluate : 1.277 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: E 934 ASN cc_start: 0.9325 (t0) cc_final: 0.8959 (p0) REVERT: E 950 TRP cc_start: 0.7635 (m100) cc_final: 0.7369 (m100) REVERT: E 979 MET cc_start: 0.8986 (tpt) cc_final: 0.8676 (tpp) REVERT: E 998 ASP cc_start: 0.7532 (m-30) cc_final: 0.6724 (m-30) REVERT: K 135 TRP cc_start: 0.8712 (t60) cc_final: 0.8341 (t60) REVERT: K 194 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8130 (tm-30) REVERT: K 199 PHE cc_start: 0.9295 (t80) cc_final: 0.9002 (t80) REVERT: K 439 THR cc_start: 0.5901 (OUTLIER) cc_final: 0.5620 (p) REVERT: K 483 LYS cc_start: 0.9298 (mptt) cc_final: 0.8560 (mtmt) REVERT: M 139 ARG cc_start: 0.8853 (mmp-170) cc_final: 0.8088 (mtt180) REVERT: M 147 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7459 (mp0) REVERT: N 123 ARG cc_start: 0.8103 (mtt90) cc_final: 0.7777 (mtt90) REVERT: F 120 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8270 (mm-30) REVERT: F 223 GLU cc_start: 0.9670 (tt0) cc_final: 0.9463 (tm-30) REVERT: F 266 CYS cc_start: 0.8180 (p) cc_final: 0.7973 (p) REVERT: F 291 LYS cc_start: 0.8124 (pttp) cc_final: 0.6847 (mmmt) REVERT: B 54 ASP cc_start: 0.7907 (p0) cc_final: 0.7413 (p0) REVERT: B 83 ASP cc_start: 0.8290 (t0) cc_final: 0.7934 (t0) REVERT: B 319 ASN cc_start: 0.9000 (t0) cc_final: 0.8753 (t0) REVERT: B 320 TRP cc_start: 0.8455 (m100) cc_final: 0.8110 (m100) REVERT: B 354 ASP cc_start: 0.8910 (m-30) cc_final: 0.8081 (t0) REVERT: A 149 ASN cc_start: 0.9125 (m-40) cc_final: 0.8743 (m-40) REVERT: A 154 LEU cc_start: 0.8701 (tp) cc_final: 0.8223 (tp) REVERT: A 194 GLN cc_start: 0.9005 (mt0) cc_final: 0.8715 (mt0) REVERT: A 195 VAL cc_start: 0.8455 (m) cc_final: 0.7510 (p) REVERT: A 233 GLU cc_start: 0.7741 (tp30) cc_final: 0.7389 (tp30) REVERT: A 291 MET cc_start: 0.8293 (tpp) cc_final: 0.7235 (mmp) outliers start: 4 outliers final: 0 residues processed: 239 average time/residue: 0.2136 time to fit residues: 72.0886 Evaluate side-chains 168 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN A 48 GLN A 109 ASN A 269 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10658 Z= 0.270 Angle : 0.806 10.566 14519 Z= 0.421 Chirality : 0.050 0.274 1686 Planarity : 0.004 0.043 1879 Dihedral : 8.043 46.009 1491 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 25.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.19 % Favored : 81.81 % Rotamer: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -4.02 (0.20), residues: 1385 helix: -1.14 (0.31), residues: 249 sheet: -2.73 (0.38), residues: 155 loop : -3.34 (0.17), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 135 HIS 0.008 0.002 HIS B 71 PHE 0.022 0.002 PHE A 58 TYR 0.019 0.002 TYR F 344 ARG 0.004 0.001 ARG E 841 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.221 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: E 934 ASN cc_start: 0.9241 (t0) cc_final: 0.8870 (p0) REVERT: K 194 GLU cc_start: 0.8682 (mm-30) cc_final: 0.7939 (tm-30) REVERT: K 238 LEU cc_start: 0.8874 (tp) cc_final: 0.8634 (tp) REVERT: K 483 LYS cc_start: 0.9218 (mptt) cc_final: 0.8592 (mtpt) REVERT: M 135 LEU cc_start: 0.8662 (pp) cc_final: 0.8237 (pp) REVERT: M 139 ARG cc_start: 0.8872 (mmp-170) cc_final: 0.8157 (mtt180) REVERT: M 147 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7408 (mp0) REVERT: M 156 TYR cc_start: 0.8677 (t80) cc_final: 0.7973 (t80) REVERT: N 123 ARG cc_start: 0.8238 (mtt90) cc_final: 0.7910 (mtt180) REVERT: F 266 CYS cc_start: 0.8422 (p) cc_final: 0.8174 (p) REVERT: F 291 LYS cc_start: 0.7933 (pttp) cc_final: 0.6692 (mmmt) REVERT: B 83 ASP cc_start: 0.8300 (t0) cc_final: 0.7887 (t0) REVERT: B 106 LYS cc_start: 0.8572 (tttp) cc_final: 0.8289 (mtmm) REVERT: B 319 ASN cc_start: 0.8970 (t0) cc_final: 0.8723 (t0) REVERT: B 347 LYS cc_start: 0.8415 (mttt) cc_final: 0.7947 (mppt) REVERT: B 354 ASP cc_start: 0.9004 (m-30) cc_final: 0.7889 (t0) REVERT: A 107 LYS cc_start: 0.9276 (mtpt) cc_final: 0.8802 (mtpt) REVERT: A 109 ASN cc_start: 0.9455 (m110) cc_final: 0.8873 (m-40) REVERT: A 127 ASN cc_start: 0.9364 (t0) cc_final: 0.9161 (t0) REVERT: A 149 ASN cc_start: 0.9273 (m-40) cc_final: 0.8790 (m-40) REVERT: A 154 LEU cc_start: 0.8737 (tp) cc_final: 0.8256 (tp) REVERT: A 195 VAL cc_start: 0.8659 (m) cc_final: 0.7806 (p) REVERT: A 199 GLU cc_start: 0.8850 (pm20) cc_final: 0.8587 (pm20) REVERT: A 228 GLN cc_start: 0.8040 (mm110) cc_final: 0.7830 (mm110) REVERT: A 238 HIS cc_start: 0.7789 (p-80) cc_final: 0.7422 (p-80) REVERT: A 241 CYS cc_start: 0.8303 (p) cc_final: 0.7478 (m) REVERT: A 291 MET cc_start: 0.8377 (tpp) cc_final: 0.7300 (tpp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2056 time to fit residues: 59.7084 Evaluate side-chains 152 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 126 optimal weight: 0.0040 chunk 134 optimal weight: 0.0070 chunk 66 optimal weight: 6.9990 chunk 120 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 overall best weight: 0.7012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN F 311 ASN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10658 Z= 0.186 Angle : 0.750 10.739 14519 Z= 0.384 Chirality : 0.048 0.227 1686 Planarity : 0.004 0.043 1879 Dihedral : 7.319 41.993 1491 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.10 % Favored : 83.90 % Rotamer: Outliers : 0.10 % Allowed : 3.86 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.72 (0.20), residues: 1385 helix: -0.61 (0.32), residues: 248 sheet: -2.71 (0.37), residues: 174 loop : -3.18 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 135 HIS 0.004 0.001 HIS B 199 PHE 0.016 0.002 PHE B 58 TYR 0.015 0.001 TYR B 40 ARG 0.004 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 1.161 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: E 934 ASN cc_start: 0.9241 (t0) cc_final: 0.8876 (p0) REVERT: K 113 VAL cc_start: 0.7276 (t) cc_final: 0.6986 (t) REVERT: K 194 GLU cc_start: 0.8559 (mm-30) cc_final: 0.7961 (tm-30) REVERT: K 202 TYR cc_start: 0.7432 (p90) cc_final: 0.6307 (p90) REVERT: K 216 GLU cc_start: 0.8143 (pp20) cc_final: 0.7925 (pm20) REVERT: K 439 THR cc_start: 0.4758 (OUTLIER) cc_final: 0.4447 (p) REVERT: K 478 LEU cc_start: 0.8743 (mt) cc_final: 0.8098 (tp) REVERT: K 483 LYS cc_start: 0.9108 (mptt) cc_final: 0.8451 (mtpt) REVERT: M 139 ARG cc_start: 0.8933 (mmp-170) cc_final: 0.8187 (mtt180) REVERT: M 147 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7376 (mp0) REVERT: M 156 TYR cc_start: 0.8627 (t80) cc_final: 0.8052 (t80) REVERT: F 291 LYS cc_start: 0.8029 (pttp) cc_final: 0.6798 (mmmt) REVERT: B 30 GLU cc_start: 0.6851 (tt0) cc_final: 0.6536 (tp30) REVERT: B 54 ASP cc_start: 0.8256 (p0) cc_final: 0.7196 (p0) REVERT: B 83 ASP cc_start: 0.8266 (t0) cc_final: 0.7857 (t0) REVERT: B 106 LYS cc_start: 0.8584 (tttp) cc_final: 0.8213 (mtpp) REVERT: B 121 GLN cc_start: 0.8820 (mt0) cc_final: 0.8592 (mt0) REVERT: B 354 ASP cc_start: 0.9006 (m-30) cc_final: 0.7954 (t0) REVERT: A 107 LYS cc_start: 0.9092 (mtpt) cc_final: 0.8428 (mtpt) REVERT: A 109 ASN cc_start: 0.9372 (m110) cc_final: 0.8727 (m-40) REVERT: A 149 ASN cc_start: 0.9230 (m-40) cc_final: 0.8754 (m-40) REVERT: A 154 LEU cc_start: 0.8749 (tp) cc_final: 0.8472 (tp) REVERT: A 195 VAL cc_start: 0.8570 (m) cc_final: 0.7870 (p) REVERT: A 199 GLU cc_start: 0.8784 (pm20) cc_final: 0.8474 (pm20) REVERT: A 238 HIS cc_start: 0.7485 (p-80) cc_final: 0.7273 (p-80) REVERT: A 241 CYS cc_start: 0.8218 (p) cc_final: 0.7263 (m) REVERT: A 291 MET cc_start: 0.8249 (tpp) cc_final: 0.7002 (mmm) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.2001 time to fit residues: 65.7125 Evaluate side-chains 160 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 92 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN B 6 GLN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN A 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10658 Z= 0.228 Angle : 0.741 8.673 14519 Z= 0.384 Chirality : 0.047 0.222 1686 Planarity : 0.004 0.044 1879 Dihedral : 7.124 41.588 1491 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.82 % Favored : 83.18 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.67 (0.20), residues: 1385 helix: -0.71 (0.31), residues: 255 sheet: -2.72 (0.39), residues: 153 loop : -3.12 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 135 HIS 0.006 0.001 HIS A 285 PHE 0.019 0.002 PHE B 58 TYR 0.017 0.002 TYR B 364 ARG 0.004 0.000 ARG K 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.287 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: E 934 ASN cc_start: 0.9207 (t0) cc_final: 0.8851 (p0) REVERT: K 117 TYR cc_start: 0.5679 (m-10) cc_final: 0.5419 (m-80) REVERT: K 194 GLU cc_start: 0.8630 (mm-30) cc_final: 0.7838 (tm-30) REVERT: K 216 GLU cc_start: 0.8266 (pp20) cc_final: 0.8028 (pm20) REVERT: M 135 LEU cc_start: 0.8573 (pp) cc_final: 0.8363 (pp) REVERT: M 139 ARG cc_start: 0.8867 (mmp-170) cc_final: 0.8143 (mtt180) REVERT: M 147 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7447 (mp0) REVERT: M 156 TYR cc_start: 0.8665 (t80) cc_final: 0.7958 (t80) REVERT: F 291 LYS cc_start: 0.7922 (pttp) cc_final: 0.6600 (mmmt) REVERT: B 30 GLU cc_start: 0.7032 (tt0) cc_final: 0.6676 (tp30) REVERT: B 54 ASP cc_start: 0.8393 (p0) cc_final: 0.7212 (p0) REVERT: B 83 ASP cc_start: 0.8279 (t0) cc_final: 0.7881 (t0) REVERT: B 121 GLN cc_start: 0.8849 (mt0) cc_final: 0.8453 (mt0) REVERT: B 347 LYS cc_start: 0.8360 (mttt) cc_final: 0.8009 (mppt) REVERT: B 354 ASP cc_start: 0.9046 (m-30) cc_final: 0.8030 (t0) REVERT: A 54 HIS cc_start: 0.7082 (m90) cc_final: 0.6874 (m-70) REVERT: A 107 LYS cc_start: 0.9255 (mtpt) cc_final: 0.8584 (mtpt) REVERT: A 109 ASN cc_start: 0.9404 (m110) cc_final: 0.8789 (m-40) REVERT: A 142 VAL cc_start: 0.9273 (p) cc_final: 0.8961 (m) REVERT: A 149 ASN cc_start: 0.9244 (m-40) cc_final: 0.8769 (m-40) REVERT: A 154 LEU cc_start: 0.8751 (tp) cc_final: 0.8478 (tp) REVERT: A 195 VAL cc_start: 0.8583 (m) cc_final: 0.7931 (p) REVERT: A 199 GLU cc_start: 0.8818 (pm20) cc_final: 0.8497 (pm20) REVERT: A 233 GLU cc_start: 0.8188 (tp30) cc_final: 0.7815 (tp30) REVERT: A 238 HIS cc_start: 0.7625 (p-80) cc_final: 0.7376 (p-80) REVERT: A 241 CYS cc_start: 0.8311 (p) cc_final: 0.7354 (m) REVERT: A 291 MET cc_start: 0.8335 (tpp) cc_final: 0.7106 (mmm) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2204 time to fit residues: 63.7518 Evaluate side-chains 155 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 0.0470 chunk 134 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 821 ASN ** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 ASN ** M 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10658 Z= 0.195 Angle : 0.731 10.525 14519 Z= 0.374 Chirality : 0.047 0.263 1686 Planarity : 0.004 0.046 1879 Dihedral : 6.923 40.012 1491 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.96 % Favored : 84.04 % Rotamer: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.55 (0.21), residues: 1385 helix: -0.51 (0.32), residues: 257 sheet: -2.50 (0.41), residues: 144 loop : -3.10 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 183 HIS 0.009 0.001 HIS B 71 PHE 0.019 0.002 PHE B 58 TYR 0.017 0.002 TYR K 436 ARG 0.007 0.000 ARG E 980 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 1.209 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: E 934 ASN cc_start: 0.9184 (t0) cc_final: 0.8826 (p0) REVERT: K 117 TYR cc_start: 0.5448 (m-10) cc_final: 0.5221 (m-80) REVERT: K 194 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7844 (tm-30) REVERT: K 483 LYS cc_start: 0.9148 (mptt) cc_final: 0.8542 (mttm) REVERT: M 135 LEU cc_start: 0.8689 (pp) cc_final: 0.8188 (pp) REVERT: M 139 ARG cc_start: 0.8912 (mmp-170) cc_final: 0.8080 (mtt180) REVERT: M 147 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7447 (mp0) REVERT: F 291 LYS cc_start: 0.7822 (pttp) cc_final: 0.6518 (mmmt) REVERT: B 30 GLU cc_start: 0.6874 (tt0) cc_final: 0.6577 (tp30) REVERT: B 54 ASP cc_start: 0.8371 (p0) cc_final: 0.7869 (p0) REVERT: B 83 ASP cc_start: 0.8227 (t0) cc_final: 0.7826 (t0) REVERT: B 106 LYS cc_start: 0.8628 (tttp) cc_final: 0.8367 (mtmm) REVERT: B 121 GLN cc_start: 0.8879 (mt0) cc_final: 0.8469 (mt0) REVERT: B 229 LEU cc_start: 0.9624 (mt) cc_final: 0.9419 (mt) REVERT: B 354 ASP cc_start: 0.9049 (m-30) cc_final: 0.8116 (t0) REVERT: A 54 HIS cc_start: 0.7209 (m90) cc_final: 0.6920 (m-70) REVERT: A 107 LYS cc_start: 0.9217 (mtpt) cc_final: 0.8533 (mtpt) REVERT: A 109 ASN cc_start: 0.9385 (m110) cc_final: 0.8782 (m-40) REVERT: A 142 VAL cc_start: 0.9272 (p) cc_final: 0.8952 (m) REVERT: A 149 ASN cc_start: 0.9263 (m-40) cc_final: 0.8805 (m-40) REVERT: A 154 LEU cc_start: 0.8589 (tp) cc_final: 0.8291 (tp) REVERT: A 173 CYS cc_start: 0.8976 (m) cc_final: 0.8759 (m) REVERT: A 195 VAL cc_start: 0.8550 (m) cc_final: 0.7875 (p) REVERT: A 199 GLU cc_start: 0.8809 (pm20) cc_final: 0.8511 (pm20) REVERT: A 238 HIS cc_start: 0.7614 (p-80) cc_final: 0.7384 (p-80) REVERT: A 241 CYS cc_start: 0.8252 (p) cc_final: 0.7272 (m) REVERT: A 291 MET cc_start: 0.8296 (tpp) cc_final: 0.7059 (mmm) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.2078 time to fit residues: 59.5728 Evaluate side-chains 157 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 113 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 821 ASN ** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10658 Z= 0.208 Angle : 0.726 9.453 14519 Z= 0.374 Chirality : 0.047 0.215 1686 Planarity : 0.004 0.045 1879 Dihedral : 6.824 38.818 1491 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.53 % Favored : 83.39 % Rotamer: Outliers : 0.19 % Allowed : 2.90 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.55 (0.21), residues: 1385 helix: -0.38 (0.32), residues: 255 sheet: -2.68 (0.38), residues: 171 loop : -3.09 (0.18), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP K 135 HIS 0.010 0.001 HIS B 71 PHE 0.020 0.002 PHE B 58 TYR 0.016 0.002 TYR F 344 ARG 0.003 0.000 ARG K 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 198 time to evaluate : 1.223 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: E 825 PHE cc_start: 0.7155 (m-10) cc_final: 0.6855 (m-10) REVERT: E 934 ASN cc_start: 0.9176 (t0) cc_final: 0.8801 (p0) REVERT: E 999 GLU cc_start: 0.7555 (pt0) cc_final: 0.7321 (pt0) REVERT: K 117 TYR cc_start: 0.5563 (m-10) cc_final: 0.5253 (m-10) REVERT: K 483 LYS cc_start: 0.9172 (mptt) cc_final: 0.8509 (mttm) REVERT: M 135 LEU cc_start: 0.8721 (pp) cc_final: 0.8280 (pp) REVERT: M 139 ARG cc_start: 0.9022 (mmp-170) cc_final: 0.8351 (mmt180) REVERT: M 147 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7407 (mp0) REVERT: N 123 ARG cc_start: 0.7996 (mtt90) cc_final: 0.7718 (mmt180) REVERT: F 291 LYS cc_start: 0.7770 (pttp) cc_final: 0.6431 (mmmt) REVERT: B 30 GLU cc_start: 0.6961 (tt0) cc_final: 0.6618 (tp30) REVERT: B 54 ASP cc_start: 0.8328 (p0) cc_final: 0.7166 (p0) REVERT: B 83 ASP cc_start: 0.8245 (t0) cc_final: 0.7835 (t0) REVERT: B 121 GLN cc_start: 0.8831 (mt0) cc_final: 0.8467 (mt0) REVERT: B 347 LYS cc_start: 0.8534 (mttt) cc_final: 0.7998 (mppt) REVERT: B 354 ASP cc_start: 0.9064 (m-30) cc_final: 0.8116 (t0) REVERT: A 54 HIS cc_start: 0.7100 (m90) cc_final: 0.6885 (m-70) REVERT: A 107 LYS cc_start: 0.9270 (mtpt) cc_final: 0.8554 (mtpt) REVERT: A 109 ASN cc_start: 0.9416 (m110) cc_final: 0.8818 (m-40) REVERT: A 142 VAL cc_start: 0.9290 (p) cc_final: 0.8965 (m) REVERT: A 149 ASN cc_start: 0.9272 (m-40) cc_final: 0.8924 (m-40) REVERT: A 195 VAL cc_start: 0.8554 (m) cc_final: 0.7896 (p) REVERT: A 233 GLU cc_start: 0.8267 (tp30) cc_final: 0.7979 (tp30) REVERT: A 238 HIS cc_start: 0.7751 (p-80) cc_final: 0.7546 (p-80) REVERT: A 241 CYS cc_start: 0.8233 (p) cc_final: 0.7822 (t) REVERT: A 291 MET cc_start: 0.8286 (tpp) cc_final: 0.6869 (mmm) outliers start: 2 outliers final: 1 residues processed: 199 average time/residue: 0.2150 time to fit residues: 61.0674 Evaluate side-chains 151 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 821 ASN ** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10658 Z= 0.184 Angle : 0.718 11.960 14519 Z= 0.365 Chirality : 0.047 0.298 1686 Planarity : 0.004 0.048 1879 Dihedral : 6.533 36.233 1491 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.23 % Favored : 84.69 % Rotamer: Outliers : 0.10 % Allowed : 1.16 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.39 (0.21), residues: 1385 helix: -0.12 (0.33), residues: 250 sheet: -2.48 (0.40), residues: 148 loop : -3.04 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 135 HIS 0.008 0.001 HIS B 71 PHE 0.020 0.002 PHE B 58 TYR 0.023 0.002 TYR A 260 ARG 0.007 0.000 ARG K 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 1.359 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: E 815 ASP cc_start: 0.9027 (t0) cc_final: 0.8481 (t0) REVERT: E 819 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8963 (mm-30) REVERT: E 825 PHE cc_start: 0.7033 (m-10) cc_final: 0.6696 (m-10) REVERT: E 934 ASN cc_start: 0.9175 (t0) cc_final: 0.8813 (p0) REVERT: K 117 TYR cc_start: 0.5474 (m-10) cc_final: 0.5139 (m-10) REVERT: K 483 LYS cc_start: 0.9121 (mptt) cc_final: 0.8389 (mttm) REVERT: M 139 ARG cc_start: 0.9029 (mmp-170) cc_final: 0.8727 (mmt180) REVERT: M 147 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7444 (mp0) REVERT: N 123 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7776 (mmp80) REVERT: F 291 LYS cc_start: 0.7735 (pttp) cc_final: 0.6406 (mmmt) REVERT: B 30 GLU cc_start: 0.6834 (tt0) cc_final: 0.6548 (tp30) REVERT: B 54 ASP cc_start: 0.8335 (p0) cc_final: 0.7134 (p0) REVERT: B 83 ASP cc_start: 0.8160 (t0) cc_final: 0.7706 (t0) REVERT: B 121 GLN cc_start: 0.8843 (mt0) cc_final: 0.8425 (mt0) REVERT: B 229 LEU cc_start: 0.9585 (mt) cc_final: 0.9342 (mt) REVERT: B 325 MET cc_start: 0.8635 (mmp) cc_final: 0.7364 (ppp) REVERT: B 347 LYS cc_start: 0.8524 (mttt) cc_final: 0.7994 (mppt) REVERT: B 354 ASP cc_start: 0.9064 (m-30) cc_final: 0.8140 (t0) REVERT: A 26 GLN cc_start: 0.9027 (mp10) cc_final: 0.8821 (mp10) REVERT: A 54 HIS cc_start: 0.7028 (m90) cc_final: 0.6801 (m-70) REVERT: A 107 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8480 (mtpt) REVERT: A 109 ASN cc_start: 0.9378 (m110) cc_final: 0.8825 (m-40) REVERT: A 142 VAL cc_start: 0.9309 (p) cc_final: 0.8995 (m) REVERT: A 149 ASN cc_start: 0.9248 (m-40) cc_final: 0.8946 (m-40) REVERT: A 195 VAL cc_start: 0.8599 (m) cc_final: 0.8204 (p) REVERT: A 233 GLU cc_start: 0.8299 (tp30) cc_final: 0.7964 (tp30) REVERT: A 238 HIS cc_start: 0.7648 (p-80) cc_final: 0.7430 (p-80) REVERT: A 241 CYS cc_start: 0.8066 (p) cc_final: 0.7149 (m) REVERT: A 260 TYR cc_start: 0.5498 (t80) cc_final: 0.5028 (t80) REVERT: A 291 MET cc_start: 0.8216 (tpp) cc_final: 0.6823 (mmm) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.2209 time to fit residues: 68.4646 Evaluate side-chains 147 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 75 optimal weight: 0.0870 chunk 54 optimal weight: 0.0670 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 821 ASN ** E1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN B 21 HIS ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10658 Z= 0.187 Angle : 0.719 11.088 14519 Z= 0.368 Chirality : 0.047 0.279 1686 Planarity : 0.004 0.047 1879 Dihedral : 6.421 36.081 1491 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.67 % Favored : 84.26 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.39 (0.21), residues: 1385 helix: -0.14 (0.33), residues: 254 sheet: -2.71 (0.38), residues: 168 loop : -2.99 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP K 135 HIS 0.009 0.001 HIS B 71 PHE 0.021 0.002 PHE B 58 TYR 0.019 0.002 TYR E 984 ARG 0.006 0.000 ARG K 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 815 ASP cc_start: 0.9012 (t0) cc_final: 0.8449 (t0) REVERT: E 819 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8939 (mm-30) REVERT: E 825 PHE cc_start: 0.7068 (m-10) cc_final: 0.6813 (m-10) REVERT: E 934 ASN cc_start: 0.9130 (t0) cc_final: 0.8787 (p0) REVERT: K 117 TYR cc_start: 0.5499 (m-10) cc_final: 0.5247 (m-10) REVERT: K 483 LYS cc_start: 0.9086 (mptt) cc_final: 0.8344 (mttm) REVERT: M 135 LEU cc_start: 0.8613 (pp) cc_final: 0.8321 (pt) REVERT: M 139 ARG cc_start: 0.8968 (mmp-170) cc_final: 0.8379 (mmt180) REVERT: M 147 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7382 (mp0) REVERT: N 123 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7819 (mmp80) REVERT: F 291 LYS cc_start: 0.7805 (pttp) cc_final: 0.6472 (mmmt) REVERT: B 30 GLU cc_start: 0.6905 (tt0) cc_final: 0.6476 (tp30) REVERT: B 54 ASP cc_start: 0.8329 (p0) cc_final: 0.7190 (p0) REVERT: B 83 ASP cc_start: 0.8045 (t0) cc_final: 0.7687 (t0) REVERT: B 121 GLN cc_start: 0.8816 (mt0) cc_final: 0.8366 (mt0) REVERT: B 199 HIS cc_start: 0.7167 (t70) cc_final: 0.6493 (t70) REVERT: B 229 LEU cc_start: 0.9573 (mt) cc_final: 0.9346 (mt) REVERT: B 325 MET cc_start: 0.8586 (mmp) cc_final: 0.7382 (ppp) REVERT: B 347 LYS cc_start: 0.8527 (mttt) cc_final: 0.8002 (mppt) REVERT: B 354 ASP cc_start: 0.9073 (m-30) cc_final: 0.8174 (t0) REVERT: A 26 GLN cc_start: 0.8997 (mp10) cc_final: 0.8786 (mp10) REVERT: A 54 HIS cc_start: 0.7114 (m90) cc_final: 0.6853 (m-70) REVERT: A 107 LYS cc_start: 0.9239 (mtpt) cc_final: 0.8535 (mtpt) REVERT: A 109 ASN cc_start: 0.9398 (m110) cc_final: 0.8895 (m-40) REVERT: A 142 VAL cc_start: 0.9327 (p) cc_final: 0.9012 (m) REVERT: A 149 ASN cc_start: 0.9242 (m-40) cc_final: 0.8939 (m-40) REVERT: A 195 VAL cc_start: 0.8610 (m) cc_final: 0.8313 (p) REVERT: A 233 GLU cc_start: 0.8233 (tp30) cc_final: 0.7901 (tp30) REVERT: A 238 HIS cc_start: 0.7657 (p-80) cc_final: 0.7432 (p-80) REVERT: A 241 CYS cc_start: 0.8080 (p) cc_final: 0.7140 (m) REVERT: A 291 MET cc_start: 0.8186 (tpp) cc_final: 0.6797 (mmm) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2064 time to fit residues: 60.4571 Evaluate side-chains 143 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 7.9990 chunk 62 optimal weight: 0.0040 chunk 91 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 85 optimal weight: 0.0020 chunk 67 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 821 ASN ** E1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN A 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10658 Z= 0.181 Angle : 0.712 11.722 14519 Z= 0.362 Chirality : 0.046 0.266 1686 Planarity : 0.004 0.049 1879 Dihedral : 6.269 33.674 1491 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.81 % Favored : 84.12 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.29 (0.21), residues: 1385 helix: 0.10 (0.33), residues: 253 sheet: -2.55 (0.38), residues: 170 loop : -2.98 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 135 HIS 0.008 0.001 HIS B 71 PHE 0.023 0.001 PHE B 58 TYR 0.020 0.002 TYR E 984 ARG 0.005 0.000 ARG K 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 815 ASP cc_start: 0.9027 (t0) cc_final: 0.8472 (t0) REVERT: E 819 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8942 (mm-30) REVERT: E 825 PHE cc_start: 0.7081 (m-10) cc_final: 0.6860 (m-10) REVERT: E 934 ASN cc_start: 0.9129 (t0) cc_final: 0.8793 (p0) REVERT: K 92 MET cc_start: 0.4467 (pmm) cc_final: 0.3353 (pmm) REVERT: K 97 ARG cc_start: 0.7840 (mpp80) cc_final: 0.7581 (mpp80) REVERT: K 117 TYR cc_start: 0.5874 (m-10) cc_final: 0.5569 (m-10) REVERT: K 483 LYS cc_start: 0.8984 (mptt) cc_final: 0.8299 (mttm) REVERT: M 147 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7434 (mp0) REVERT: F 291 LYS cc_start: 0.7958 (pttp) cc_final: 0.6618 (mmmt) REVERT: B 30 GLU cc_start: 0.6786 (tt0) cc_final: 0.6439 (tp30) REVERT: B 54 ASP cc_start: 0.8418 (p0) cc_final: 0.7213 (p0) REVERT: B 83 ASP cc_start: 0.8008 (t0) cc_final: 0.7661 (t0) REVERT: B 121 GLN cc_start: 0.8828 (mt0) cc_final: 0.8391 (mt0) REVERT: B 199 HIS cc_start: 0.7231 (t70) cc_final: 0.6555 (t70) REVERT: B 229 LEU cc_start: 0.9568 (mt) cc_final: 0.9334 (mt) REVERT: B 347 LYS cc_start: 0.8524 (mttt) cc_final: 0.7998 (mppt) REVERT: B 354 ASP cc_start: 0.9081 (m-30) cc_final: 0.8138 (t0) REVERT: A 26 GLN cc_start: 0.8991 (mp10) cc_final: 0.8773 (mp10) REVERT: A 54 HIS cc_start: 0.7136 (m90) cc_final: 0.6878 (m-70) REVERT: A 107 LYS cc_start: 0.9210 (mtpt) cc_final: 0.8538 (mtpt) REVERT: A 109 ASN cc_start: 0.9381 (m110) cc_final: 0.8890 (m-40) REVERT: A 142 VAL cc_start: 0.9329 (p) cc_final: 0.9042 (m) REVERT: A 149 ASN cc_start: 0.9229 (m-40) cc_final: 0.8978 (m-40) REVERT: A 195 VAL cc_start: 0.8555 (m) cc_final: 0.8328 (p) REVERT: A 233 GLU cc_start: 0.8241 (tp30) cc_final: 0.7948 (tp30) REVERT: A 238 HIS cc_start: 0.7587 (p-80) cc_final: 0.7381 (p-80) REVERT: A 241 CYS cc_start: 0.7866 (p) cc_final: 0.6993 (m) REVERT: A 291 MET cc_start: 0.8098 (tpp) cc_final: 0.6776 (mmm) outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.1969 time to fit residues: 57.6945 Evaluate side-chains 145 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 0.0570 chunk 46 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 821 ASN ** E1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN B 404 ASN A 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.078411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.067053 restraints weight = 64015.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.068774 restraints weight = 42406.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.070013 restraints weight = 30882.587| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10658 Z= 0.306 Angle : 0.787 12.118 14519 Z= 0.409 Chirality : 0.049 0.266 1686 Planarity : 0.005 0.044 1879 Dihedral : 6.825 36.425 1491 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 27.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 18.34 % Favored : 81.59 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.48 (0.21), residues: 1385 helix: -0.31 (0.32), residues: 252 sheet: -2.58 (0.38), residues: 171 loop : -3.06 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP K 135 HIS 0.006 0.002 HIS A 95 PHE 0.029 0.002 PHE K 199 TYR 0.022 0.002 TYR E 984 ARG 0.006 0.001 ARG K 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.88 seconds wall clock time: 43 minutes 50.74 seconds (2630.74 seconds total)