Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 22:17:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7e_32342/04_2023/7w7e_32342_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7e_32342/04_2023/7w7e_32342.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7e_32342/04_2023/7w7e_32342_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7e_32342/04_2023/7w7e_32342_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7e_32342/04_2023/7w7e_32342_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7e_32342/04_2023/7w7e_32342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7e_32342/04_2023/7w7e_32342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7e_32342/04_2023/7w7e_32342_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7e_32342/04_2023/7w7e_32342_updated.pdb" } resolution = 3.4 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= 0.074 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 59 5.16 5 C 5440 2.51 5 N 1449 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 208": "OE1" <-> "OE2" Residue "H TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 222": "OE1" <-> "OE2" Residue "H TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 77": "NH1" <-> "NH2" Residue "R TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 160": "NH1" <-> "NH2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 164": "NH1" <-> "NH2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R ASP 207": "OD1" <-> "OD2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 240": "NH1" <-> "NH2" Residue "R ARG 243": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R ARG 386": "NH1" <-> "NH2" Residue "R PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8524 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1649 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "H" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2097 Unusual residues: {'W58': 1} Classifications: {'peptide': 260, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 250, None: 1} Not linked: pdbres="CYS R 457 " pdbres="W58 R 501 " Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 4.90, per 1000 atoms: 0.57 Number of scatterers: 8524 At special positions: 0 Unit cell: (91.8, 115.6, 124.95, 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 59 16.00 O 1576 8.00 N 1449 7.00 C 5440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.4 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2036 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 14 sheets defined 32.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 7 through 30 removed outlier: 4.267A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 209 through 216 removed outlier: 5.296A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N CYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE A 216 " --> pdb=" O TRP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 297 through 311 removed outlier: 3.685A pdb=" N ALA A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 347 Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.826A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 45 removed outlier: 3.847A pdb=" N ALA G 45 " --> pdb=" O CYS G 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'R' and resid 46 through 75 removed outlier: 3.601A pdb=" N PHE R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 110 removed outlier: 4.024A pdb=" N LEU R 85 " --> pdb=" O PRO R 82 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE R 86 " --> pdb=" O GLN R 83 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE R 102 " --> pdb=" O THR R 99 " (cutoff:3.500A) Proline residue: R 103 - end of helix removed outlier: 3.941A pdb=" N VAL R 110 " --> pdb=" O ALA R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 151 removed outlier: 4.014A pdb=" N LEU R 139 " --> pdb=" O SER R 135 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 159 removed outlier: 3.786A pdb=" N LYS R 159 " --> pdb=" O GLU R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 180 Processing helix chain 'R' and resid 209 through 219 removed outlier: 4.131A pdb=" N ILE R 213 " --> pdb=" O LYS R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 241 removed outlier: 3.536A pdb=" N ILE R 234 " --> pdb=" O VAL R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 414 removed outlier: 4.076A pdb=" N GLU R 384 " --> pdb=" O ARG R 380 " (cutoff:3.500A) Proline residue: R 404 - end of helix removed outlier: 4.105A pdb=" N VAL R 414 " --> pdb=" O THR R 410 " (cutoff:3.500A) Processing helix chain 'R' and resid 422 through 442 removed outlier: 3.672A pdb=" N SER R 434 " --> pdb=" O GLY R 430 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER R 435 " --> pdb=" O TYR R 431 " (cutoff:3.500A) Proline residue: R 438 - end of helix Processing helix chain 'R' and resid 446 through 456 Processing sheet with id= A, first strand: chain 'A' and resid 34 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 222 through 225 Processing sheet with id= C, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.615A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.950A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.528A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 190 through 192 Processing sheet with id= G, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.939A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 295 through 298 removed outlier: 3.639A pdb=" N LEU B 286 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.027A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.792A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 92 through 94 Processing sheet with id= L, first strand: chain 'H' and resid 214 through 219 removed outlier: 3.787A pdb=" N ILE H 177 " --> pdb=" O TRP H 164 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU H 166 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU H 175 " --> pdb=" O LEU H 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 193 through 195 Processing sheet with id= N, first strand: chain 'H' and resid 34 through 37 removed outlier: 3.807A pdb=" N TRP H 36 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 855 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: 2.23 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1372 1.31 - 1.44: 2436 1.44 - 1.56: 4813 1.56 - 1.68: 1 1.68 - 1.81: 82 Bond restraints: 8704 Sorted by residual: bond pdb=" C LEU R 125 " pdb=" O LEU R 125 " ideal model delta sigma weight residual 1.236 1.288 -0.052 1.18e-02 7.18e+03 1.94e+01 bond pdb=" C1 W58 R 501 " pdb=" C2 W58 R 501 " ideal model delta sigma weight residual 1.566 1.491 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C LEU R 127 " pdb=" O LEU R 127 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.17e-02 7.31e+03 1.23e+01 bond pdb=" N ILE G 28 " pdb=" CA ILE G 28 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.17e+01 bond pdb=" N ILE G 25 " pdb=" CA ILE G 25 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.11e+01 ... (remaining 8699 not shown) Histogram of bond angle deviations from ideal: 89.67 - 101.77: 23 101.77 - 113.87: 5059 113.87 - 125.97: 6578 125.97 - 138.08: 132 138.08 - 150.18: 2 Bond angle restraints: 11794 Sorted by residual: angle pdb=" C SER H 133 " pdb=" N SER H 134 " pdb=" CA SER H 134 " ideal model delta sigma weight residual 121.50 133.33 -11.83 1.43e+00 4.89e-01 6.84e+01 angle pdb=" C ALA B 309 " pdb=" N GLY B 310 " pdb=" CA GLY B 310 " ideal model delta sigma weight residual 120.00 127.46 -7.46 1.10e+00 8.26e-01 4.60e+01 angle pdb=" N TYR R 409 " pdb=" CA TYR R 409 " pdb=" C TYR R 409 " ideal model delta sigma weight residual 111.07 104.64 6.43 1.07e+00 8.73e-01 3.62e+01 angle pdb=" C ASP R 128 " pdb=" N VAL R 129 " pdb=" CA VAL R 129 " ideal model delta sigma weight residual 120.56 113.46 7.10 1.26e+00 6.30e-01 3.17e+01 angle pdb=" C ASP R 128 " pdb=" CA ASP R 128 " pdb=" CB ASP R 128 " ideal model delta sigma weight residual 110.88 102.43 8.45 1.57e+00 4.06e-01 2.90e+01 ... (remaining 11789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.71: 4812 23.71 - 47.41: 294 47.41 - 71.12: 21 71.12 - 94.83: 7 94.83 - 118.53: 3 Dihedral angle restraints: 5137 sinusoidal: 1982 harmonic: 3155 Sorted by residual: dihedral pdb=" CB CYS R 121 " pdb=" SG CYS R 121 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual 93.00 171.50 -78.50 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" C ASP R 128 " pdb=" N ASP R 128 " pdb=" CA ASP R 128 " pdb=" CB ASP R 128 " ideal model delta harmonic sigma weight residual -122.60 -111.52 -11.08 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" CA ARG R 420 " pdb=" C ARG R 420 " pdb=" N THR R 421 " pdb=" CA THR R 421 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 5134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1227 0.074 - 0.148: 102 0.148 - 0.222: 7 0.222 - 0.296: 3 0.296 - 0.370: 2 Chirality restraints: 1341 Sorted by residual: chirality pdb=" CA TYR H 223 " pdb=" N TYR H 223 " pdb=" C TYR H 223 " pdb=" CB TYR H 223 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA TYR R 409 " pdb=" N TYR R 409 " pdb=" C TYR R 409 " pdb=" CB TYR R 409 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA ASP R 128 " pdb=" N ASP R 128 " pdb=" C ASP R 128 " pdb=" CB ASP R 128 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1338 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 123 " -0.026 2.00e-02 2.50e+03 5.26e-02 2.77e+01 pdb=" C ILE R 123 " 0.091 2.00e-02 2.50e+03 pdb=" O ILE R 123 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR R 124 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 22 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C GLU G 22 " 0.072 2.00e-02 2.50e+03 pdb=" O GLU G 22 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA G 23 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 220 " -0.012 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C HIS H 220 " 0.045 2.00e-02 2.50e+03 pdb=" O HIS H 220 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU H 221 " -0.015 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 216 2.68 - 3.23: 8672 3.23 - 3.79: 12220 3.79 - 4.34: 16392 4.34 - 4.90: 27783 Nonbonded interactions: 65283 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.120 2.440 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.153 2.440 nonbonded pdb=" N GLU R 122 " pdb=" OE1 GLU R 122 " model vdw 2.187 2.520 nonbonded pdb=" O ILE H 145 " pdb=" OG1 THR H 201 " model vdw 2.206 2.440 nonbonded pdb=" O GLY H 16 " pdb=" OG SER H 17 " model vdw 2.227 2.440 ... (remaining 65278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.860 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: 7.650 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.080 Find NCS groups from input model: 0.240 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 8704 Z= 0.259 Angle : 0.656 11.829 11794 Z= 0.420 Chirality : 0.046 0.370 1341 Planarity : 0.003 0.053 1488 Dihedral : 14.408 118.533 3095 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.27), residues: 1068 helix: 1.90 (0.29), residues: 337 sheet: -2.75 (0.34), residues: 218 loop : -2.31 (0.26), residues: 513 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.051 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 179 average time/residue: 0.2461 time to fit residues: 57.8255 Evaluate side-chains 132 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1183 time to fit residues: 1.5206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 239 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 HIS R 446 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 8704 Z= 0.433 Angle : 0.736 7.941 11794 Z= 0.384 Chirality : 0.047 0.187 1341 Planarity : 0.005 0.053 1488 Dihedral : 6.992 93.944 1185 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.26), residues: 1068 helix: 1.40 (0.28), residues: 343 sheet: -2.64 (0.32), residues: 241 loop : -2.29 (0.27), residues: 484 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.086 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 149 average time/residue: 0.2320 time to fit residues: 46.5662 Evaluate side-chains 131 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1171 time to fit residues: 4.2681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.0670 chunk 96 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 0.1980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8704 Z= 0.166 Angle : 0.590 7.746 11794 Z= 0.307 Chirality : 0.042 0.216 1341 Planarity : 0.004 0.045 1488 Dihedral : 5.535 76.205 1185 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.27), residues: 1068 helix: 1.76 (0.29), residues: 343 sheet: -2.22 (0.32), residues: 243 loop : -2.19 (0.28), residues: 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 0.986 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 146 average time/residue: 0.2242 time to fit residues: 44.3977 Evaluate side-chains 126 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1064 time to fit residues: 1.9388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 GLN R 446 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8704 Z= 0.173 Angle : 0.566 7.157 11794 Z= 0.296 Chirality : 0.042 0.184 1341 Planarity : 0.004 0.061 1488 Dihedral : 5.099 80.611 1185 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.27), residues: 1068 helix: 1.80 (0.29), residues: 343 sheet: -1.96 (0.33), residues: 238 loop : -2.15 (0.27), residues: 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 151 average time/residue: 0.2133 time to fit residues: 44.2921 Evaluate side-chains 136 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0803 time to fit residues: 3.1173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.1980 chunk 58 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 446 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 8704 Z= 0.207 Angle : 0.579 7.978 11794 Z= 0.303 Chirality : 0.042 0.163 1341 Planarity : 0.004 0.055 1488 Dihedral : 5.171 85.908 1185 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.27), residues: 1068 helix: 1.88 (0.29), residues: 341 sheet: -1.85 (0.33), residues: 237 loop : -2.08 (0.28), residues: 490 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.004 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 145 average time/residue: 0.2104 time to fit residues: 41.8304 Evaluate side-chains 131 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0833 time to fit residues: 2.6962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 0.0670 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8704 Z= 0.171 Angle : 0.561 8.280 11794 Z= 0.293 Chirality : 0.041 0.158 1341 Planarity : 0.004 0.063 1488 Dihedral : 5.002 82.457 1185 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.27), residues: 1068 helix: 1.91 (0.29), residues: 340 sheet: -1.76 (0.32), residues: 247 loop : -2.05 (0.28), residues: 481 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 0.997 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 140 average time/residue: 0.2290 time to fit residues: 44.0874 Evaluate side-chains 133 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0850 time to fit residues: 2.6548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 75 optimal weight: 0.0570 chunk 87 optimal weight: 0.0010 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 overall best weight: 0.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 8704 Z= 0.152 Angle : 0.550 9.392 11794 Z= 0.287 Chirality : 0.041 0.157 1341 Planarity : 0.004 0.058 1488 Dihedral : 4.852 79.991 1185 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.27), residues: 1068 helix: 1.95 (0.29), residues: 343 sheet: -1.60 (0.33), residues: 235 loop : -2.03 (0.28), residues: 490 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 0.938 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 135 average time/residue: 0.2199 time to fit residues: 40.3207 Evaluate side-chains 130 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0790 time to fit residues: 1.7102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 20 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 433 ASN R 446 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8704 Z= 0.228 Angle : 0.585 9.327 11794 Z= 0.307 Chirality : 0.042 0.163 1341 Planarity : 0.004 0.063 1488 Dihedral : 5.025 81.894 1185 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.27), residues: 1068 helix: 1.88 (0.29), residues: 339 sheet: -1.69 (0.32), residues: 249 loop : -2.07 (0.28), residues: 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.971 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 135 average time/residue: 0.2275 time to fit residues: 41.9486 Evaluate side-chains 134 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0974 time to fit residues: 2.6629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8704 Z= 0.181 Angle : 0.573 10.124 11794 Z= 0.298 Chirality : 0.041 0.158 1341 Planarity : 0.004 0.061 1488 Dihedral : 4.926 80.817 1185 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.27), residues: 1068 helix: 1.90 (0.29), residues: 342 sheet: -1.59 (0.32), residues: 249 loop : -2.05 (0.28), residues: 477 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 0.988 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 135 average time/residue: 0.2349 time to fit residues: 43.0996 Evaluate side-chains 129 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0844 time to fit residues: 1.7067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8704 Z= 0.176 Angle : 0.579 10.531 11794 Z= 0.301 Chirality : 0.041 0.165 1341 Planarity : 0.004 0.063 1488 Dihedral : 4.865 79.896 1185 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.27), residues: 1068 helix: 1.87 (0.29), residues: 344 sheet: -1.43 (0.33), residues: 241 loop : -2.00 (0.28), residues: 483 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 0.973 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 131 average time/residue: 0.2310 time to fit residues: 40.9878 Evaluate side-chains 132 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0886 time to fit residues: 1.6965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 0.0040 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.141174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.104801 restraints weight = 14296.827| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.01 r_work: 0.3258 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 8704 Z= 0.157 Angle : 0.569 10.913 11794 Z= 0.293 Chirality : 0.041 0.163 1341 Planarity : 0.004 0.063 1488 Dihedral : 4.735 77.100 1185 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.27), residues: 1068 helix: 1.97 (0.29), residues: 344 sheet: -1.34 (0.33), residues: 235 loop : -2.01 (0.28), residues: 489 =============================================================================== Job complete usr+sys time: 1987.04 seconds wall clock time: 36 minutes 52.27 seconds (2212.27 seconds total)