Starting phenix.real_space_refine (version: dev) on Sun Feb 19 08:40:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/02_2023/7wk0_32554.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/02_2023/7wk0_32554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/02_2023/7wk0_32554.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/02_2023/7wk0_32554.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/02_2023/7wk0_32554.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk0_32554/02_2023/7wk0_32554.pdb" } resolution = 3.32 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= 0.000 sd= 0.010 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 Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "F ARG 346": "NH1" <-> "NH2" Residue "F ARG 408": "NH1" <-> "NH2" Residue "F ARG 454": "NH1" <-> "NH2" Residue "F ARG 457": "NH1" <-> "NH2" Residue "F ARG 466": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9724 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1699 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "B" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "C" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1572 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1699 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "E" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "F" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1572 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.07, per 1000 atoms: 0.62 Number of scatterers: 9724 At special positions: 0 Unit cell: (88.312, 155.344, 110.656, 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 34 16.00 O 1890 8.00 N 1646 7.00 C 6154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " 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 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " " NAG F 601 " - " ASN F 343 " Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.7 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 25 sheets defined 2.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.131A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.804A pdb=" N GLU B 126 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.567A pdb=" N ASP E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 82' Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.798A pdb=" N GLN F 506 " --> pdb=" O VAL F 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 60 removed outlier: 5.936A pdb=" N GLY A 50 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR A 60 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 48 " --> pdb=" O TYR A 60 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 92 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 94 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 120 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.873A pdb=" N GLY A 152 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.507A pdb=" N THR A 164 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS A 209 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS A 222 " --> pdb=" O CYS A 209 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 220 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS A 213 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 218 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.868A pdb=" N VAL B 10 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.747A pdb=" N ILE B 74 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 20 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 117 through 120 removed outlier: 3.503A pdb=" N ILE B 138 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 176 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 140 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR B 174 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.752A pdb=" N THR B 147 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS B 195 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 206 " --> pdb=" O CYS B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.726A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.726A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.534A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.628A pdb=" N TYR D 94 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL D 48 " --> pdb=" O TYR D 60 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR D 60 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY D 50 " --> pdb=" O ILE D 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.533A pdb=" N LEU D 151 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 193 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER D 192 " --> pdb=" O PHE D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 Processing sheet with id=AB8, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.887A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'E' and resid 44 through 47 removed outlier: 5.626A pdb=" N LEU E 45 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN E 36 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E 47 " --> pdb=" O TRP E 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 117 through 120 removed outlier: 3.899A pdb=" N VAL E 135 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE E 138 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP E 140 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR E 174 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 194 through 196 removed outlier: 3.674A pdb=" N CYS E 195 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS E 206 " --> pdb=" O CYS E 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 357 through 358 removed outlier: 4.190A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA F 435 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 357 through 358 removed outlier: 4.190A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'F' and resid 473 through 474 183 hydrogen bonds defined for protein. 447 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: 2.65 Time building geometry restraints manager: 4.04 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: 1593 1.31 - 1.44: 2884 1.44 - 1.56: 5469 1.56 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 9982 Sorted by residual: bond pdb=" CA LYS D 65 " pdb=" C LYS D 65 " ideal model delta sigma weight residual 1.524 1.445 0.079 1.31e-02 5.83e+03 3.62e+01 bond pdb=" N ASN C 448 " pdb=" CA ASN C 448 " ideal model delta sigma weight residual 1.455 1.397 0.059 1.25e-02 6.40e+03 2.19e+01 bond pdb=" N GLU F 406 " pdb=" CA GLU F 406 " ideal model delta sigma weight residual 1.457 1.405 0.052 1.16e-02 7.43e+03 2.02e+01 bond pdb=" C ILE C 358 " pdb=" O ILE C 358 " ideal model delta sigma weight residual 1.237 1.188 0.050 1.13e-02 7.83e+03 1.93e+01 bond pdb=" CA ASN C 354 " pdb=" C ASN C 354 " ideal model delta sigma weight residual 1.523 1.469 0.053 1.23e-02 6.61e+03 1.89e+01 ... (remaining 9977 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.41: 450 107.41 - 114.06: 5473 114.06 - 120.71: 3689 120.71 - 127.36: 3881 127.36 - 134.01: 121 Bond angle restraints: 13614 Sorted by residual: angle pdb=" N ASN C 370 " pdb=" CA ASN C 370 " pdb=" C ASN C 370 " ideal model delta sigma weight residual 114.31 104.48 9.83 1.29e+00 6.01e-01 5.81e+01 angle pdb=" N VAL F 407 " pdb=" CA VAL F 407 " pdb=" C VAL F 407 " ideal model delta sigma weight residual 111.58 104.58 7.00 1.06e+00 8.90e-01 4.36e+01 angle pdb=" N GLY D 66 " pdb=" CA GLY D 66 " pdb=" C GLY D 66 " ideal model delta sigma weight residual 115.27 107.54 7.73 1.41e+00 5.03e-01 3.00e+01 angle pdb=" N ASN C 448 " pdb=" CA ASN C 448 " pdb=" C ASN C 448 " ideal model delta sigma weight residual 109.24 101.13 8.11 1.67e+00 3.59e-01 2.36e+01 angle pdb=" N SER C 359 " pdb=" CA SER C 359 " pdb=" C SER C 359 " ideal model delta sigma weight residual 108.74 114.66 -5.92 1.38e+00 5.25e-01 1.84e+01 ... (remaining 13609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5548 17.71 - 35.42: 304 35.42 - 53.14: 45 53.14 - 70.85: 16 70.85 - 88.56: 1 Dihedral angle restraints: 5914 sinusoidal: 2258 harmonic: 3656 Sorted by residual: dihedral pdb=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N SER B 192 " pdb=" CA SER B 192 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" N ASN C 448 " pdb=" C ASN C 448 " pdb=" CA ASN C 448 " pdb=" CB ASN C 448 " ideal model delta harmonic sigma weight residual 122.80 111.49 11.31 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" CA GLU A 161 " pdb=" C GLU A 161 " pdb=" N PRO A 162 " pdb=" CA PRO A 162 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 5911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1322 0.071 - 0.142: 169 0.142 - 0.212: 4 0.212 - 0.283: 2 0.283 - 0.354: 1 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA LYS D 65 " pdb=" N LYS D 65 " pdb=" C LYS D 65 " pdb=" CB LYS D 65 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA ASN F 448 " pdb=" N ASN F 448 " pdb=" C ASN F 448 " pdb=" CB ASN F 448 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ALA C 372 " pdb=" N ALA C 372 " pdb=" C ALA C 372 " pdb=" CB ALA C 372 " both_signs ideal model delta sigma weight residual False 2.48 2.27 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1495 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 601 " 0.257 2.00e-02 2.50e+03 2.18e-01 5.92e+02 pdb=" C7 NAG F 601 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG F 601 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG F 601 " -0.371 2.00e-02 2.50e+03 pdb=" O7 NAG F 601 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 400 " -0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C PHE C 400 " 0.075 2.00e-02 2.50e+03 pdb=" O PHE C 400 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL C 401 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 353 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C TRP C 353 " -0.058 2.00e-02 2.50e+03 pdb=" O TRP C 353 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN C 354 " 0.020 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1603 2.77 - 3.30: 9290 3.30 - 3.83: 15901 3.83 - 4.37: 18585 4.37 - 4.90: 31950 Nonbonded interactions: 77329 Sorted by model distance: nonbonded pdb=" OG SER E 62 " pdb=" OG1 THR E 73 " model vdw 2.233 2.440 nonbonded pdb=" OG SER B 64 " pdb=" OG1 THR B 71 " model vdw 2.263 2.440 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.272 2.440 nonbonded pdb=" OD2 ASP E 91 " pdb=" OG SER E 94 " model vdw 2.278 2.440 nonbonded pdb=" OE1 GLU E 126 " pdb=" OG1 THR E 133 " model vdw 2.286 2.440 ... (remaining 77324 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 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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 34 5.16 5 C 6154 2.51 5 N 1646 2.21 5 O 1890 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=1.00 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: 5.610 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: 22.220 Check model and map are aligned: 0.140 Process input model: 28.360 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 0.079 9982 Z= 0.267 Angle : 0.651 9.922 13614 Z= 0.393 Chirality : 0.045 0.354 1498 Planarity : 0.007 0.218 1764 Dihedral : 11.022 88.559 3538 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.22 % Favored : 87.54 % Rotamer Outliers : 7.71 % 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: -4.96 (0.20), residues: 1252 helix: -5.35 (0.10), residues: 70 sheet: -2.88 (0.22), residues: 452 loop : -3.46 (0.19), residues: 730 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 237 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 35 residues processed: 296 average time/residue: 0.2440 time to fit residues: 97.3856 Evaluate side-chains 232 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 197 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1991 time to fit residues: 11.3742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 59 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 33 HIS B 88 GLN B 190 HIS C 409 GLN C 437 ASN C 481 ASN D 3 GLN D 118 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 172 ASN F 409 GLN ** F 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 9982 Z= 0.361 Angle : 0.666 7.551 13614 Z= 0.343 Chirality : 0.046 0.227 1498 Planarity : 0.005 0.054 1764 Dihedral : 5.061 29.612 1390 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer Outliers : 4.04 % 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: -4.21 (0.21), residues: 1252 helix: -5.01 (0.30), residues: 56 sheet: -2.26 (0.24), residues: 416 loop : -3.07 (0.19), residues: 780 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 230 time to evaluate : 0.996 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 260 average time/residue: 0.2755 time to fit residues: 97.0672 Evaluate side-chains 231 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 209 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1068 time to fit residues: 6.1334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 121 optimal weight: 0.0980 chunk 100 optimal weight: 0.0060 chunk 111 optimal weight: 0.3980 chunk 38 optimal weight: 0.1980 chunk 90 optimal weight: 0.8980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 168 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 ASN F 450 ASN F 481 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 9982 Z= 0.262 Angle : 0.626 7.802 13614 Z= 0.319 Chirality : 0.045 0.204 1498 Planarity : 0.005 0.051 1764 Dihedral : 5.025 30.670 1390 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.38 % Favored : 87.54 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.78 (0.22), residues: 1252 helix: -4.99 (0.27), residues: 56 sheet: -1.85 (0.26), residues: 398 loop : -2.81 (0.20), residues: 798 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 1.029 Fit side-chains outliers start: 30 outliers final: 9 residues processed: 230 average time/residue: 0.2140 time to fit residues: 68.5107 Evaluate side-chains 219 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 210 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1127 time to fit residues: 3.0387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 37 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN F 481 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.080 9982 Z= 0.503 Angle : 0.745 11.018 13614 Z= 0.382 Chirality : 0.049 0.214 1498 Planarity : 0.005 0.055 1764 Dihedral : 5.787 49.160 1390 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.34 % Favored : 84.58 % Rotamer Outliers : 3.38 % 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: -3.62 (0.22), residues: 1252 helix: -5.03 (0.24), residues: 56 sheet: -1.73 (0.25), residues: 432 loop : -2.72 (0.21), residues: 764 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 1.146 Fit side-chains outliers start: 36 outliers final: 15 residues processed: 239 average time/residue: 0.2281 time to fit residues: 76.2924 Evaluate side-chains 226 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 211 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0945 time to fit residues: 4.2372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.0040 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 89 optimal weight: 0.0870 chunk 49 optimal weight: 0.5980 chunk 102 optimal weight: 0.0270 chunk 82 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.2228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 172 ASN C 394 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 9982 Z= 0.222 Angle : 0.639 8.885 13614 Z= 0.323 Chirality : 0.045 0.195 1498 Planarity : 0.005 0.053 1764 Dihedral : 5.370 46.528 1390 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.78 % Favored : 87.14 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.23), residues: 1252 helix: -5.01 (0.28), residues: 44 sheet: -1.41 (0.26), residues: 404 loop : -2.57 (0.21), residues: 804 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 1.162 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 225 average time/residue: 0.2326 time to fit residues: 72.4340 Evaluate side-chains 224 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1244 time to fit residues: 4.3312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 119 optimal weight: 0.9980 chunk 99 optimal weight: 0.0470 chunk 55 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN C 394 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 9982 Z= 0.395 Angle : 0.707 10.088 13614 Z= 0.358 Chirality : 0.046 0.216 1498 Planarity : 0.005 0.051 1764 Dihedral : 5.641 51.815 1390 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.06 % Favored : 85.86 % Rotamer Outliers : 2.63 % 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: -3.26 (0.23), residues: 1252 helix: -5.01 (0.28), residues: 44 sheet: -1.35 (0.25), residues: 436 loop : -2.60 (0.21), residues: 772 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 212 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 21 residues processed: 225 average time/residue: 0.2311 time to fit residues: 71.8673 Evaluate side-chains 239 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 218 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1460 time to fit residues: 6.3486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 119 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN C 394 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 9982 Z= 0.387 Angle : 0.706 11.087 13614 Z= 0.357 Chirality : 0.047 0.208 1498 Planarity : 0.005 0.049 1764 Dihedral : 5.731 54.362 1390 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.06 % Favored : 85.86 % Rotamer Outliers : 1.50 % 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: -3.21 (0.23), residues: 1252 helix: -4.96 (0.30), residues: 44 sheet: -1.34 (0.26), residues: 410 loop : -2.53 (0.21), residues: 798 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 224 time to evaluate : 1.171 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 232 average time/residue: 0.2303 time to fit residues: 74.3801 Evaluate side-chains 221 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 213 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0884 time to fit residues: 2.8867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN D 74 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 9982 Z= 0.313 Angle : 0.692 12.790 13614 Z= 0.347 Chirality : 0.046 0.205 1498 Planarity : 0.005 0.049 1764 Dihedral : 5.644 53.691 1390 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.74 % Favored : 86.18 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.11 (0.23), residues: 1252 helix: -4.95 (0.29), residues: 44 sheet: -1.22 (0.26), residues: 412 loop : -2.48 (0.21), residues: 796 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 213 time to evaluate : 1.352 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 219 average time/residue: 0.2322 time to fit residues: 70.6212 Evaluate side-chains 218 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 212 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1414 time to fit residues: 3.0251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.1980 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 0.0870 chunk 87 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 105 optimal weight: 0.2980 chunk 110 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 9982 Z= 0.293 Angle : 0.693 13.478 13614 Z= 0.348 Chirality : 0.046 0.201 1498 Planarity : 0.005 0.047 1764 Dihedral : 5.582 52.648 1390 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.34 % Favored : 86.58 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.07 (0.23), residues: 1252 helix: -4.95 (0.28), residues: 44 sheet: -1.12 (0.26), residues: 418 loop : -2.51 (0.21), residues: 790 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 201 time to evaluate : 0.973 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 206 average time/residue: 0.2235 time to fit residues: 63.4005 Evaluate side-chains 206 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0945 time to fit residues: 3.0156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.0030 chunk 71 optimal weight: 0.4980 chunk 55 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 0.0000 chunk 75 optimal weight: 0.6980 chunk 60 optimal weight: 0.0870 chunk 78 optimal weight: 0.2980 overall best weight: 0.1572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 9982 Z= 0.200 Angle : 0.656 14.702 13614 Z= 0.326 Chirality : 0.045 0.209 1498 Planarity : 0.005 0.046 1764 Dihedral : 5.316 48.009 1390 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.86 (0.23), residues: 1252 helix: -4.84 (0.30), residues: 32 sheet: -0.93 (0.27), residues: 398 loop : -2.42 (0.20), residues: 822 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.971 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2490 time to fit residues: 65.4972 Evaluate side-chains 187 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 0.0030 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113496 restraints weight = 14293.889| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.30 r_work: 0.3274 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 9982 Z= 0.307 Angle : 0.695 13.986 13614 Z= 0.348 Chirality : 0.046 0.225 1498 Planarity : 0.005 0.048 1764 Dihedral : 5.495 49.900 1390 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.42 % Favored : 86.50 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.88 (0.23), residues: 1252 helix: -4.89 (0.28), residues: 32 sheet: -1.04 (0.26), residues: 418 loop : -2.40 (0.21), residues: 802 =============================================================================== Job complete usr+sys time: 2830.66 seconds wall clock time: 52 minutes 21.68 seconds (3141.68 seconds total)