Starting phenix.real_space_refine (version: dev) on Thu May 12 23:18:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/05_2022/6n9u_0379_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/05_2022/6n9u_0379.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/05_2022/6n9u_0379_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/05_2022/6n9u_0379_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/05_2022/6n9u_0379_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/05_2022/6n9u_0379.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/05_2022/6n9u_0379.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/05_2022/6n9u_0379_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/05_2022/6n9u_0379_updated.pdb" } resolution = 3.7 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 248": "NH1" <-> "NH2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 255": "NH1" <-> "NH2" Residue "H ARG 429": "NH1" <-> "NH2" Residue "H ARG 547": "NH1" <-> "NH2" Residue "H ARG 566": "NH1" <-> "NH2" Residue "H ARG 591": "NH1" <-> "NH2" Residue "H ARG 599": "NH1" <-> "NH2" Residue "H TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 687": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 8822 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1740 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1538 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "H" Number of atoms: 5144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5144 Classifications: {'peptide': 645} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 622, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "P" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {'DOC': 1} Classifications: {'undetermined': 1, 'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {None: 1, 'rna3p': 4} Not linked: pdbres=" G P 5 " pdbres="DOC P 6 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "T" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'TTP': 1, ' MG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69 SG CYS E 17 59.453 36.079 46.143 1.00 84.80 S ATOM 91 SG CYS E 20 58.126 33.933 44.451 1.00 85.19 S ATOM 204 SG CYS E 36 56.118 35.082 46.849 1.00 66.69 S ATOM 229 SG CYS E 39 58.279 32.837 47.885 1.00 69.94 S Time building chain proxies: 5.53, per 1000 atoms: 0.63 Number of scatterers: 8822 At special positions: 0 Unit cell: (86.86, 100.62, 121.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 47 16.00 P 20 15.00 Mg 2 11.99 O 1694 8.00 N 1531 7.00 C 5527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 235 " - pdb=" SG CYS F 241 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 17 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 39 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 36 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 20 " Number of angles added : 6 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 11 sheets defined 30.9% alpha, 10.6% beta 5 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'E' and resid 88 through 94 Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 160 through 169 Processing helix chain 'E' and resid 188 through 191 No H-bonds generated for 'chain 'E' and resid 188 through 191' Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 238 through 244 removed outlier: 3.744A pdb=" N ASN E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 255 removed outlier: 4.490A pdb=" N GLU E 252 " --> pdb=" O GLU E 249 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL E 254 " --> pdb=" O MET E 251 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP E 255 " --> pdb=" O GLU E 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 94 Processing helix chain 'F' and resid 160 through 168 removed outlier: 3.601A pdb=" N VAL F 165 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 192 removed outlier: 3.647A pdb=" N ALA F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'F' and resid 238 through 243 Processing helix chain 'F' and resid 250 through 253 No H-bonds generated for 'chain 'F' and resid 250 through 253' Processing helix chain 'H' and resid 39 through 51 Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.527A pdb=" N LYS H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 98 No H-bonds generated for 'chain 'H' and resid 95 through 98' Processing helix chain 'H' and resid 125 through 131 Processing helix chain 'H' and resid 139 through 150 Processing helix chain 'H' and resid 165 through 185 removed outlier: 3.856A pdb=" N LYS H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 230 removed outlier: 3.635A pdb=" N GLU H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 246 removed outlier: 3.917A pdb=" N LEU H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 258 No H-bonds generated for 'chain 'H' and resid 255 through 258' Processing helix chain 'H' and resid 341 through 347 Processing helix chain 'H' and resid 377 through 399 removed outlier: 3.926A pdb=" N ALA H 381 " --> pdb=" O PRO H 377 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP H 384 " --> pdb=" O GLN H 380 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 408 No H-bonds generated for 'chain 'H' and resid 406 through 408' Processing helix chain 'H' and resid 449 through 452 No H-bonds generated for 'chain 'H' and resid 449 through 452' Processing helix chain 'H' and resid 479 through 487 removed outlier: 3.642A pdb=" N ALA H 485 " --> pdb=" O LEU H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 505 through 513 Processing helix chain 'H' and resid 518 through 529 removed outlier: 3.722A pdb=" N TYR H 526 " --> pdb=" O LYS H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 545 through 556 removed outlier: 4.054A pdb=" N LYS H 552 " --> pdb=" O GLY H 548 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 573 Processing helix chain 'H' and resid 609 through 636 removed outlier: 4.130A pdb=" N SER H 616 " --> pdb=" O THR H 612 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H 617 " --> pdb=" O LEU H 613 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU H 620 " --> pdb=" O SER H 616 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE H 621 " --> pdb=" O ALA H 617 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS H 622 " --> pdb=" O GLY H 618 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE H 627 " --> pdb=" O LYS H 623 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU H 630 " --> pdb=" O ILE H 626 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU H 633 " --> pdb=" O THR H 629 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU H 635 " --> pdb=" O GLU H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 663 through 683 removed outlier: 4.577A pdb=" N GLN H 674 " --> pdb=" O ILE H 670 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU H 675 " --> pdb=" O GLU H 671 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 34 through 36 removed outlier: 3.667A pdb=" N TYR E 13 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 96 through 99 removed outlier: 3.740A pdb=" N SER E 120 " --> pdb=" O TYR E 111 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 175 through 177 removed outlier: 7.986A pdb=" N VAL E 176 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN E 201 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL E 155 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE E 203 " --> pdb=" O VAL E 155 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 97 through 100 removed outlier: 4.018A pdb=" N SER F 120 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 153 through 155 Processing sheet with id= F, first strand: chain 'H' and resid 32 through 34 removed outlier: 4.188A pdb=" N GLY H 21 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU H 7 " --> pdb=" O HIS H 19 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY H 21 " --> pdb=" O ASP H 5 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP H 5 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE H 23 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL H 3 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 264 through 267 Processing sheet with id= H, first strand: chain 'H' and resid 419 through 421 Processing sheet with id= I, first strand: chain 'H' and resid 692 through 697 removed outlier: 3.685A pdb=" N ALA H 650 " --> pdb=" O GLN H 657 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY H 659 " --> pdb=" O TYR H 648 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TYR H 648 " --> pdb=" O GLY H 659 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 592 through 594 Processing sheet with id= K, first strand: chain 'H' and resid 574 through 579 removed outlier: 4.182A pdb=" N GLU H 575 " --> pdb=" O LYS H 587 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LYS H 587 " --> pdb=" O GLU H 575 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER H 577 " --> pdb=" O GLN H 585 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN H 585 " --> pdb=" O SER H 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= K 225 hydrogen bonds defined for protein. 636 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1466 1.31 - 1.44: 2556 1.44 - 1.56: 4926 1.56 - 1.69: 37 1.69 - 1.82: 72 Bond restraints: 9057 Sorted by residual: bond pdb=" C4' DOC P 6 " pdb=" C3' DOC P 6 " ideal model delta sigma weight residual 1.316 1.516 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C4' DOC P 6 " pdb=" O4' DOC P 6 " ideal model delta sigma weight residual 1.635 1.442 0.193 2.00e-02 2.50e+03 9.33e+01 bond pdb=" O4' DOC P 6 " pdb=" C1' DOC P 6 " ideal model delta sigma weight residual 1.269 1.416 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C2 DOC P 6 " pdb=" N3 DOC P 6 " ideal model delta sigma weight residual 1.482 1.374 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C5 DOC P 6 " pdb=" C6 DOC P 6 " ideal model delta sigma weight residual 1.481 1.377 0.104 2.00e-02 2.50e+03 2.73e+01 ... (remaining 9052 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.41: 309 106.41 - 113.31: 4743 113.31 - 120.21: 3526 120.21 - 127.12: 3586 127.12 - 134.02: 159 Bond angle restraints: 12323 Sorted by residual: angle pdb=" N ILE H 464 " pdb=" CA ILE H 464 " pdb=" C ILE H 464 " ideal model delta sigma weight residual 113.71 109.54 4.17 9.50e-01 1.11e+00 1.93e+01 angle pdb=" N GLY F 134 " pdb=" CA GLY F 134 " pdb=" C GLY F 134 " ideal model delta sigma weight residual 110.29 115.14 -4.85 1.28e+00 6.10e-01 1.44e+01 angle pdb=" C ALA H 513 " pdb=" N GLU H 514 " pdb=" CA GLU H 514 " ideal model delta sigma weight residual 122.08 127.17 -5.09 1.47e+00 4.63e-01 1.20e+01 angle pdb=" N PHE E 206 " pdb=" CA PHE E 206 " pdb=" C PHE E 206 " ideal model delta sigma weight residual 110.80 117.99 -7.19 2.13e+00 2.20e-01 1.14e+01 angle pdb=" CA GLU H 514 " pdb=" CB GLU H 514 " pdb=" CG GLU H 514 " ideal model delta sigma weight residual 114.10 120.32 -6.22 2.00e+00 2.50e-01 9.67e+00 ... (remaining 12318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.27: 5167 33.27 - 66.54: 91 66.54 - 99.81: 9 99.81 - 133.07: 0 133.07 - 166.34: 1 Dihedral angle restraints: 5268 sinusoidal: 2221 harmonic: 3047 Sorted by residual: dihedral pdb=" C2 TTP H 801 " pdb=" C1' TTP H 801 " pdb=" N1 TTP H 801 " pdb=" O4' TTP H 801 " ideal model delta sinusoidal sigma weight residual 301.68 135.34 166.34 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" CA TYR H 64 " pdb=" C TYR H 64 " pdb=" N ASP H 65 " pdb=" CA ASP H 65 " ideal model delta harmonic sigma weight residual -180.00 -153.26 -26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" C5' TTP H 801 " pdb=" O5' TTP H 801 " pdb=" PA TTP H 801 " pdb=" O3A TTP H 801 " ideal model delta sinusoidal sigma weight residual 179.97 84.34 95.63 1 2.00e+01 2.50e-03 2.64e+01 ... (remaining 5265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1017 0.062 - 0.124: 250 0.124 - 0.187: 34 0.187 - 0.249: 5 0.249 - 0.311: 1 Chirality restraints: 1307 Sorted by residual: chirality pdb=" C4' TTP H 801 " pdb=" C3' TTP H 801 " pdb=" C5' TTP H 801 " pdb=" O4' TTP H 801 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE H 505 " pdb=" CA ILE H 505 " pdb=" CG1 ILE H 505 " pdb=" CG2 ILE H 505 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C1' DOC P 6 " pdb=" O4' DOC P 6 " pdb=" C2' DOC P 6 " pdb=" N1 DOC P 6 " both_signs ideal model delta sigma weight residual False 2.34 2.55 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1304 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 700 " 0.024 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP H 700 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP H 700 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP H 700 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 700 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 700 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 700 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 700 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 700 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP H 700 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 97 " 0.017 2.00e-02 2.50e+03 1.84e-02 8.46e+00 pdb=" CG TRP F 97 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP F 97 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP F 97 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 97 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 97 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 97 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 97 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 97 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 97 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 147 " 0.020 2.00e-02 2.50e+03 1.79e-02 7.97e+00 pdb=" CG TRP E 147 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP E 147 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP E 147 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 147 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 147 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 147 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 147 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 147 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP E 147 " 0.003 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 792 2.74 - 3.28: 7736 3.28 - 3.82: 13959 3.82 - 4.36: 16053 4.36 - 4.90: 27841 Nonbonded interactions: 66381 Sorted by model distance: nonbonded pdb=" OD2 ASP H 654 " pdb="MG MG H 802 " model vdw 2.205 2.170 nonbonded pdb=" O GLY F 158 " pdb=" OG SER F 177 " model vdw 2.254 2.440 nonbonded pdb=" O ALA H 476 " pdb="MG MG H 802 " model vdw 2.274 2.170 nonbonded pdb=" O2B TTP H 801 " pdb="MG MG H 802 " model vdw 2.283 2.170 nonbonded pdb=" OD2 ASP H 197 " pdb=" OG1 THR H 199 " model vdw 2.293 2.440 ... (remaining 66376 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 20 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 5527 2.51 5 N 1531 2.21 5 O 1694 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 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: 13.140 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.070 Process input model: 30.980 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.200 9057 Z= 0.451 Angle : 0.837 9.427 12323 Z= 0.450 Chirality : 0.055 0.311 1307 Planarity : 0.006 0.059 1526 Dihedral : 12.727 166.343 3315 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -4.67 (0.20), residues: 1049 helix: -3.21 (0.18), residues: 422 sheet: -2.67 (0.40), residues: 142 loop : -3.04 (0.23), residues: 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 237 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 237 average time/residue: 0.2766 time to fit residues: 83.9225 Evaluate side-chains 131 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN E 129 ASN E 201 GLN E 244 ASN E 253 GLN E 256 ASN F 136 HIS H 150 GLN ** H 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 GLN ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 520 ASN H 615 GLN ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9057 Z= 0.222 Angle : 0.583 11.070 12323 Z= 0.305 Chirality : 0.043 0.189 1307 Planarity : 0.005 0.104 1526 Dihedral : 11.674 172.463 1332 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.54 (0.23), residues: 1049 helix: -1.92 (0.23), residues: 423 sheet: -2.46 (0.40), residues: 153 loop : -2.63 (0.25), residues: 473 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.076 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 162 average time/residue: 0.2499 time to fit residues: 53.8016 Evaluate side-chains 131 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0858 time to fit residues: 4.0218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 104 optimal weight: 0.0370 chunk 85 optimal weight: 0.6980 chunk 95 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9057 Z= 0.190 Angle : 0.553 10.686 12323 Z= 0.289 Chirality : 0.042 0.170 1307 Planarity : 0.005 0.072 1526 Dihedral : 11.475 170.921 1332 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.84 (0.24), residues: 1049 helix: -1.21 (0.25), residues: 419 sheet: -2.08 (0.42), residues: 148 loop : -2.38 (0.25), residues: 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.033 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 136 average time/residue: 0.2567 time to fit residues: 46.8344 Evaluate side-chains 117 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0876 time to fit residues: 2.1976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.4980 chunk 72 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 ASN ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9057 Z= 0.185 Angle : 0.536 8.306 12323 Z= 0.276 Chirality : 0.042 0.190 1307 Planarity : 0.004 0.057 1526 Dihedral : 11.319 171.098 1332 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.39 (0.25), residues: 1049 helix: -0.77 (0.25), residues: 423 sheet: -1.82 (0.41), residues: 162 loop : -2.21 (0.26), residues: 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.057 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 134 average time/residue: 0.2399 time to fit residues: 43.4660 Evaluate side-chains 119 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1383 time to fit residues: 3.7711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 398 GLN ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 9057 Z= 0.267 Angle : 0.580 10.574 12323 Z= 0.298 Chirality : 0.044 0.165 1307 Planarity : 0.004 0.051 1526 Dihedral : 11.377 172.371 1332 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.27 (0.25), residues: 1049 helix: -0.66 (0.26), residues: 423 sheet: -1.79 (0.44), residues: 148 loop : -2.15 (0.26), residues: 478 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.066 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 130 average time/residue: 0.2364 time to fit residues: 41.9188 Evaluate side-chains 125 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0910 time to fit residues: 2.7092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN E 169 GLN H 19 HIS ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 9057 Z= 0.207 Angle : 0.540 8.963 12323 Z= 0.277 Chirality : 0.042 0.168 1307 Planarity : 0.004 0.048 1526 Dihedral : 11.196 173.098 1332 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.04 (0.26), residues: 1049 helix: -0.43 (0.26), residues: 422 sheet: -1.83 (0.44), residues: 153 loop : -2.00 (0.27), residues: 474 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.021 Fit side-chains outliers start: 12 outliers final: 2 residues processed: 124 average time/residue: 0.2432 time to fit residues: 40.8591 Evaluate side-chains 112 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0902 time to fit residues: 1.7378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 0.0870 chunk 61 optimal weight: 0.0050 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 9057 Z= 0.159 Angle : 0.515 8.511 12323 Z= 0.263 Chirality : 0.041 0.164 1307 Planarity : 0.004 0.046 1526 Dihedral : 10.991 172.829 1332 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.76 (0.26), residues: 1049 helix: -0.17 (0.27), residues: 420 sheet: -1.60 (0.42), residues: 163 loop : -1.89 (0.28), residues: 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.052 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 131 average time/residue: 0.2312 time to fit residues: 41.5035 Evaluate side-chains 112 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0955 time to fit residues: 1.7253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN E 239 ASN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 9057 Z= 0.276 Angle : 0.582 9.555 12323 Z= 0.299 Chirality : 0.044 0.155 1307 Planarity : 0.004 0.047 1526 Dihedral : 11.167 173.566 1332 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.90 (0.26), residues: 1049 helix: -0.36 (0.26), residues: 421 sheet: -1.69 (0.44), residues: 148 loop : -1.90 (0.27), residues: 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.069 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 124 average time/residue: 0.2547 time to fit residues: 42.2602 Evaluate side-chains 109 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0831 time to fit residues: 1.8281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 9057 Z= 0.238 Angle : 0.577 9.699 12323 Z= 0.293 Chirality : 0.043 0.180 1307 Planarity : 0.004 0.046 1526 Dihedral : 11.118 173.328 1332 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.79 (0.26), residues: 1049 helix: -0.26 (0.26), residues: 415 sheet: -1.56 (0.45), residues: 143 loop : -1.85 (0.27), residues: 491 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.063 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 116 average time/residue: 0.2493 time to fit residues: 39.2416 Evaluate side-chains 110 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1462 time to fit residues: 2.7351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9057 Z= 0.214 Angle : 0.573 10.049 12323 Z= 0.289 Chirality : 0.043 0.179 1307 Planarity : 0.004 0.046 1526 Dihedral : 11.024 173.317 1332 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.77 (0.26), residues: 1049 helix: -0.18 (0.27), residues: 416 sheet: -1.74 (0.43), residues: 148 loop : -1.84 (0.27), residues: 485 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 1.107 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 114 average time/residue: 0.2511 time to fit residues: 38.7381 Evaluate side-chains 110 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0948 time to fit residues: 1.9180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.0060 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139017 restraints weight = 12449.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141105 restraints weight = 8107.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142557 restraints weight = 6022.676| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.394 9057 Z= 0.284 Angle : 0.794 47.727 12323 Z= 0.384 Chirality : 0.042 0.169 1307 Planarity : 0.004 0.046 1526 Dihedral : 10.921 173.112 1332 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.59 (0.26), residues: 1049 helix: -0.03 (0.27), residues: 414 sheet: -1.64 (0.43), residues: 148 loop : -1.72 (0.28), residues: 487 =============================================================================== Job complete usr+sys time: 1913.12 seconds wall clock time: 35 minutes 27.97 seconds (2127.97 seconds total)