Starting phenix.real_space_refine (version: dev) on Mon Dec 12 12:40:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/12_2022/6bx3_7303.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/12_2022/6bx3_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_2022/6bx3_7303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/12_2022/6bx3_7303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/12_2022/6bx3_7303.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bx3_7303/12_2022/6bx3_7303.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 6.36, per 1000 atoms: 0.61 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: 4.33 Conformation dependent library (CDL) restraints added in 1.6 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: 0.43 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: 2.55 Time building geometry restraints manager: 4.66 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 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. 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: 1.580 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: 7.400 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 29.950 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 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 : 25.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 18.77 % Favored : 81.16 % Rotamer Outliers : 0.97 % 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 *********************** 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: 0.2357 time to fit residues: 93.8791 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: 0.1124 time to fit residues: 2.3385 ------------------------------------------------------------------------------- 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: 0.7202 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 14.021 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 : 25.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.33 % Favored : 82.67 % Rotamer Outliers : 0.29 % 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 *********************** 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 : 1.330 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: 0.2060 time to fit residues: 67.4168 Evaluate side-chains 150 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1359 time to fit residues: 1.9061 ------------------------------------------------------------------------------- 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: 9.9990 chunk 85 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 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: 0.7277 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 10658 Z= 0.332 Angle : 0.850 11.024 14519 Z= 0.448 Chirality : 0.051 0.326 1686 Planarity : 0.005 0.045 1879 Dihedral : 8.324 46.579 1491 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 29.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.41 % Favored : 81.59 % Rotamer Outliers : 0.10 % 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: -4.13 (0.20), residues: 1385 helix: -1.18 (0.31), residues: 251 sheet: -2.68 (0.38), residues: 158 loop : -3.46 (0.17), residues: 976 *********************** 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 200 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.398 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: 1 outliers final: 1 residues processed: 200 average time/residue: 0.2047 time to fit residues: 59.3372 Evaluate side-chains 136 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0936 time to fit residues: 1.8568 ------------------------------------------------------------------------------- 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: 6.9990 chunk 95 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 126 optimal weight: 0.0070 chunk 134 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 120 optimal weight: 0.0980 chunk 36 optimal weight: 0.1980 overall best weight: 1.2400 ------------------------------------------------------------------------------- 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** K 476 ASN ** 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10658 Z= 0.201 Angle : 0.772 12.377 14519 Z= 0.400 Chirality : 0.048 0.222 1686 Planarity : 0.004 0.045 1879 Dihedral : 7.617 43.072 1491 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.11 % Favored : 82.89 % Rotamer Outliers : 0.00 % 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: -3.79 (0.20), residues: 1385 helix: -0.60 (0.32), residues: 245 sheet: -2.60 (0.37), residues: 165 loop : -3.28 (0.18), residues: 975 *********************** 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 215 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.280 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: 215 average time/residue: 0.1977 time to fit residues: 62.1563 Evaluate side-chains 138 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6688 ------------------------------------------------------------------------------- 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: 8.9990 chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 10658 Z= 0.237 Angle : 0.761 10.555 14519 Z= 0.398 Chirality : 0.048 0.214 1686 Planarity : 0.004 0.050 1879 Dihedral : 7.374 42.595 1491 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.83 % Favored : 82.17 % Rotamer Outliers : 0.00 % 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: -3.70 (0.21), residues: 1385 helix: -0.56 (0.32), residues: 248 sheet: -2.52 (0.38), residues: 171 loop : -3.22 (0.18), residues: 966 *********************** 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 194 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.398 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: 194 average time/residue: 0.2228 time to fit residues: 65.1986 Evaluate side-chains 133 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7901 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- 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** ** M 160 GLN ** 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 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10658 Z= 0.217 Angle : 0.755 10.970 14519 Z= 0.392 Chirality : 0.048 0.279 1686 Planarity : 0.004 0.046 1879 Dihedral : 7.121 41.324 1491 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 17.33 % Favored : 82.60 % Rotamer Outliers : 0.00 % 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: -3.69 (0.21), residues: 1385 helix: -0.57 (0.32), residues: 256 sheet: -2.68 (0.38), residues: 168 loop : -3.18 (0.18), residues: 961 *********************** 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 203 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.532 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: 203 average time/residue: 0.2114 time to fit residues: 62.3320 Evaluate side-chains 131 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5089 ------------------------------------------------------------------------------- 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: 6.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 160 GLN ** 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 311 ASN B 33 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10658 Z= 0.248 Angle : 0.775 12.017 14519 Z= 0.403 Chirality : 0.048 0.258 1686 Planarity : 0.004 0.049 1879 Dihedral : 7.149 41.095 1491 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 25.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 18.48 % Favored : 81.44 % Rotamer Outliers : 0.00 % 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: -0.50 (0.32), residues: 258 sheet: -2.58 (0.39), residues: 161 loop : -3.21 (0.18), residues: 966 *********************** 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 188 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.388 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: 188 average time/residue: 0.1986 time to fit residues: 55.7131 Evaluate side-chains 125 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7452 ------------------------------------------------------------------------------- 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: 0.9980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** ** M 160 GLN ** 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 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 HIS A 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.5333 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= 0.199 Angle : 0.754 12.334 14519 Z= 0.388 Chirality : 0.048 0.317 1686 Planarity : 0.004 0.048 1879 Dihedral : 6.886 39.065 1491 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.61 % Favored : 83.32 % Rotamer Outliers : 0.00 % 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: -3.59 (0.21), residues: 1385 helix: -0.28 (0.33), residues: 253 sheet: -2.61 (0.39), residues: 158 loop : -3.19 (0.18), residues: 974 *********************** 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 188 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.247 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: 188 average time/residue: 0.1943 time to fit residues: 54.6855 Evaluate side-chains 131 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7967 ------------------------------------------------------------------------------- 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: 0.8980 chunk 117 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** ** M 160 GLN ** 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 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 HIS A 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.5579 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= 0.191 Angle : 0.739 11.894 14519 Z= 0.380 Chirality : 0.047 0.272 1686 Planarity : 0.004 0.047 1879 Dihedral : 6.574 36.908 1491 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.68 % Favored : 83.25 % Rotamer Outliers : 0.00 % 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: -0.17 (0.33), residues: 254 sheet: -2.67 (0.37), residues: 167 loop : -3.11 (0.18), residues: 964 *********************** 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 201 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.427 Fit side-chains 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: 201 average time/residue: 0.1942 time to fit residues: 58.4018 Evaluate side-chains 128 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7738 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 0.0370 chunk 91 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 127 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- 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** ** M 160 GLN ** 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 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 HIS A 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.5767 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= 0.200 Angle : 0.738 11.962 14519 Z= 0.379 Chirality : 0.047 0.272 1686 Planarity : 0.004 0.047 1879 Dihedral : 6.542 35.368 1491 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 17.11 % Favored : 82.82 % Rotamer Outliers : 0.00 % 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: -0.14 (0.33), residues: 255 sheet: -2.69 (0.38), residues: 167 loop : -3.11 (0.18), residues: 963 ********************** 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 189 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.378 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: 189 average time/residue: 0.1975 time to fit residues: 55.6959 Evaluate side-chains 131 residues out of total 1264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6595 ------------------------------------------------------------------------------- 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: 0.0770 chunk 101 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 46 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 2.9144 ------------------------------------------------------------------------------- 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** ** M 160 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN A 54 HIS A 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.079211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.067714 restraints weight = 62071.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.069514 restraints weight = 40349.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.070796 restraints weight = 29088.896| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10658 Z= 0.262 Angle : 0.772 11.561 14519 Z= 0.401 Chirality : 0.048 0.274 1686 Planarity : 0.004 0.046 1879 Dihedral : 6.754 36.370 1491 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 24.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 18.27 % Favored : 81.66 % Rotamer Outliers : 0.00 % 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: -3.59 (0.21), residues: 1385 helix: -0.26 (0.32), residues: 256 sheet: -2.73 (0.37), residues: 174 loop : -3.16 (0.18), residues: 955 =============================================================================== Job complete usr+sys time: 2287.74 seconds wall clock time: 43 minutes 2.87 seconds (2582.87 seconds total)