Starting phenix.real_space_refine on Sat Dec 9 07:34:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/12_2023/6bx3_7303.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/12_2023/6bx3_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_7303/12_2023/6bx3_7303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/12_2023/6bx3_7303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/12_2023/6bx3_7303.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/12_2023/6bx3_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-1.21rc1-5172/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: 5.81, 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: 4.30 Conformation dependent library (CDL) restraints added in 2.0 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: 0.90 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: 2.53 Time building geometry restraints manager: 4.64 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: 2.270 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: 7.020 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.130 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.800 ------------------------------------------------------------------------------- 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 : 1.231 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 outliers start: 10 outliers final: 3 residues processed: 291 average time/residue: 0.2446 time to fit residues: 97.4198 Evaluate side-chains 162 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1172 time to fit residues: 2.3865 ------------------------------------------------------------------------------- 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: 9.9990 chunk 105 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 0.0070 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- 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 6 GLN B 225 ASN B 330 ASN A 172 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10658 Z= 0.286 Angle : 0.856 14.022 14519 Z= 0.450 Chirality : 0.050 0.212 1686 Planarity : 0.005 0.047 1879 Dihedral : 8.717 49.805 1491 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 25.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.33 % Favored : 82.67 % Rotamer: Outliers : 0.29 % Allowed : 4.83 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -4.35 (0.19), residues: 1385 helix: -1.78 (0.28), residues: 253 sheet: -2.87 (0.34), residues: 185 loop : -3.47 (0.17), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 135 HIS 0.007 0.002 HIS A 285 PHE 0.019 0.002 PHE B 355 TYR 0.024 0.002 TYR M 156 ARG 0.006 0.001 ARG E 973 *********************** 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 229 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 226 time to evaluate : 1.217 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 outliers start: 3 outliers final: 1 residues processed: 227 average time/residue: 0.2181 time to fit residues: 71.0783 Evaluate side-chains 150 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1265 time to fit residues: 1.7997 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** 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: 0.7330 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10658 Z= 0.308 Angle : 0.829 10.500 14519 Z= 0.438 Chirality : 0.051 0.343 1686 Planarity : 0.005 0.044 1879 Dihedral : 8.230 46.113 1491 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.34 % Favored : 81.66 % Rotamer: Outliers : 0.10 % Allowed : 6.56 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -4.08 (0.20), residues: 1385 helix: -1.12 (0.31), residues: 252 sheet: -2.62 (0.38), residues: 158 loop : -3.44 (0.17), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP K 135 HIS 0.008 0.002 HIS B 208 PHE 0.021 0.002 PHE A 58 TYR 0.021 0.002 TYR F 344 ARG 0.005 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 204 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 204 average time/residue: 0.2118 time to fit residues: 62.4947 Evaluate side-chains 140 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0994 time to fit residues: 1.9110 ------------------------------------------------------------------------------- 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: 5.9990 chunk 95 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 60 optimal weight: 0.1980 chunk 84 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10658 Z= 0.251 Angle : 0.791 10.966 14519 Z= 0.413 Chirality : 0.049 0.218 1686 Planarity : 0.005 0.111 1879 Dihedral : 7.852 44.731 1491 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.63 % Favored : 81.37 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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: -3.88 (0.20), residues: 1385 helix: -0.71 (0.32), residues: 248 sheet: -2.61 (0.38), residues: 160 loop : -3.35 (0.17), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 135 HIS 0.006 0.002 HIS B 208 PHE 0.018 0.002 PHE B 58 TYR 0.018 0.002 TYR K 354 ARG 0.010 0.001 ARG B 128 *********************** 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 197 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.283 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 outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2195 time to fit residues: 63.3940 Evaluate side-chains 136 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5936 ------------------------------------------------------------------------------- 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: 5.9990 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** E1022 ASN K 225 ASN K 476 ASN ** 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 33 GLN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4428 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= 0.208 Angle : 0.749 10.857 14519 Z= 0.390 Chirality : 0.047 0.213 1686 Planarity : 0.004 0.044 1879 Dihedral : 7.411 42.279 1491 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.91 % Favored : 82.09 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % 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 (0.21), residues: 1385 helix: -0.39 (0.33), residues: 247 sheet: -2.54 (0.38), residues: 164 loop : -3.28 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 135 HIS 0.004 0.001 HIS B 71 PHE 0.019 0.002 PHE B 58 TYR 0.016 0.001 TYR F 344 ARG 0.004 0.001 ARG B 128 *********************** 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 202 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.302 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 outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2003 time to fit residues: 60.5516 Evaluate side-chains 135 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6492 ------------------------------------------------------------------------------- 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: 0.9980 chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 111 optimal weight: 0.0030 chunk 62 optimal weight: 0.0770 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 overall best weight: 1.0950 ------------------------------------------------------------------------------- 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** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10658 Z= 0.191 Angle : 0.749 11.235 14519 Z= 0.385 Chirality : 0.047 0.254 1686 Planarity : 0.004 0.050 1879 Dihedral : 7.041 39.983 1491 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 17.11 % Favored : 82.82 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % 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: -3.56 (0.21), residues: 1385 helix: -0.41 (0.33), residues: 255 sheet: -2.72 (0.36), residues: 184 loop : -3.08 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 183 HIS 0.009 0.001 HIS B 71 PHE 0.018 0.001 PHE B 58 TYR 0.013 0.002 TYR F 344 ARG 0.009 0.001 ARG B 128 *********************** 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 204 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.145 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 outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1986 time to fit residues: 59.2176 Evaluate side-chains 133 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6440 ------------------------------------------------------------------------------- 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: 7.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 75 optimal weight: 0.3980 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN A 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10658 Z= 0.262 Angle : 0.777 11.825 14519 Z= 0.404 Chirality : 0.048 0.249 1686 Planarity : 0.004 0.045 1879 Dihedral : 7.098 40.452 1491 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 25.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 18.05 % Favored : 81.88 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: -3.67 (0.21), residues: 1385 helix: -0.46 (0.32), residues: 257 sheet: -2.64 (0.39), residues: 159 loop : -3.21 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 183 HIS 0.012 0.002 HIS B 71 PHE 0.018 0.002 PHE A 112 TYR 0.024 0.002 TYR A 260 ARG 0.007 0.001 ARG B 128 *********************** 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 185 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.185 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 outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2193 time to fit residues: 59.6876 Evaluate side-chains 129 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7590 ------------------------------------------------------------------------------- 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: 0.0000 chunk 80 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 105 optimal weight: 0.0010 chunk 121 optimal weight: 0.3980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10658 Z= 0.184 Angle : 0.748 13.350 14519 Z= 0.383 Chirality : 0.047 0.260 1686 Planarity : 0.004 0.048 1879 Dihedral : 6.776 38.002 1491 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.60 % Favored : 84.33 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % 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: -3.50 (0.21), residues: 1385 helix: -0.23 (0.33), residues: 251 sheet: -2.52 (0.41), residues: 143 loop : -3.11 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 183 HIS 0.006 0.001 HIS B 71 PHE 0.019 0.002 PHE B 58 TYR 0.011 0.001 TYR K 354 ARG 0.004 0.000 ARG B 128 *********************** 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 195 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2076 time to fit residues: 59.9246 Evaluate side-chains 129 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5831 ------------------------------------------------------------------------------- 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: 1.9990 chunk 117 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.0040 chunk 98 optimal weight: 0.0370 chunk 38 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.5674 ------------------------------------------------------------------------------- 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** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10658 Z= 0.183 Angle : 0.756 11.666 14519 Z= 0.384 Chirality : 0.048 0.319 1686 Planarity : 0.004 0.048 1879 Dihedral : 6.518 36.795 1491 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.38 % Favored : 84.55 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -3.43 (0.21), residues: 1385 helix: -0.09 (0.33), residues: 251 sheet: -2.53 (0.40), residues: 143 loop : -3.08 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 183 HIS 0.006 0.001 HIS B 71 PHE 0.023 0.002 PHE B 58 TYR 0.016 0.001 TYR F 345 ARG 0.005 0.000 ARG B 128 *********************** 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 194 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.283 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 outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2051 time to fit residues: 58.2879 Evaluate side-chains 132 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5499 ------------------------------------------------------------------------------- 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: 0.8980 chunk 62 optimal weight: 0.3980 chunk 91 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** ** N 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.5734 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= 0.196 Angle : 0.735 11.881 14519 Z= 0.379 Chirality : 0.047 0.274 1686 Planarity : 0.004 0.048 1879 Dihedral : 6.455 34.541 1491 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.32 % Favored : 83.61 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -3.42 (0.21), residues: 1385 helix: 0.06 (0.33), residues: 251 sheet: -2.97 (0.35), residues: 177 loop : -3.01 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 320 HIS 0.009 0.001 HIS B 71 PHE 0.021 0.001 PHE B 58 TYR 0.020 0.002 TYR E 984 ARG 0.007 0.000 ARG B 128 ********************** 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 182 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.364 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 outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2064 time to fit residues: 56.3438 Evaluate side-chains 127 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6482 ------------------------------------------------------------------------------- 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: 0.3980 chunk 101 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 46 optimal weight: 0.0770 chunk 113 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 2.6944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 33 GLN ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN A 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.079902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.068467 restraints weight = 62433.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.070300 restraints weight = 40917.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.071636 restraints weight = 29570.788| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10658 Z= 0.248 Angle : 0.768 11.862 14519 Z= 0.398 Chirality : 0.048 0.283 1686 Planarity : 0.004 0.045 1879 Dihedral : 6.634 34.689 1491 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 17.11 % Favored : 82.82 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -3.45 (0.21), residues: 1385 helix: -0.00 (0.33), residues: 254 sheet: -2.71 (0.38), residues: 163 loop : -3.11 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 183 HIS 0.011 0.002 HIS B 71 PHE 0.021 0.002 PHE B 58 TYR 0.031 0.002 TYR E 984 ARG 0.009 0.001 ARG B 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.22 seconds wall clock time: 44 minutes 2.04 seconds (2642.04 seconds total)