Starting phenix.real_space_refine on Mon Mar 11 18:23:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/03_2024/6n9u_0379_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/03_2024/6n9u_0379.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/03_2024/6n9u_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_0379/03_2024/6n9u_0379_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/03_2024/6n9u_0379_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/03_2024/6n9u_0379.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/03_2024/6n9u_0379.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/03_2024/6n9u_0379_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9u_0379/03_2024/6n9u_0379_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 622} 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: {'RNA': 5, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna3p': 4, None: 1} 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: {' MG': 2, 'TTP': 1} 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: 5.25, per 1000 atoms: 0.60 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: 3.66 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal 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: 3.67 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: 2.48 Time building geometry restraints manager: 3.82 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 1.334 1.516 -0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" C4' DOC P 6 " pdb=" O4' DOC P 6 " ideal model delta sigma weight residual 1.609 1.442 0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" O4' DOC P 6 " pdb=" C1' DOC P 6 " ideal model delta sigma weight residual 1.268 1.416 -0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C4 DOC P 6 " pdb=" N4 DOC P 6 " ideal model delta sigma weight residual 1.494 1.348 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" C2 DOC P 6 " pdb=" N3 DOC P 6 " ideal model delta sigma weight residual 1.492 1.374 0.118 2.00e-02 2.50e+03 3.50e+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: 5182 33.27 - 66.54: 101 66.54 - 99.81: 11 99.81 - 133.07: 0 133.07 - 166.34: 1 Dihedral angle restraints: 5295 sinusoidal: 2248 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 5292 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 2.33 2.55 -0.21 2.00e-01 2.50e+01 1.14e+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 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: 3.820 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: 12.930 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 30.510 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 0.182 9057 Z= 0.453 Angle : 0.837 9.427 12323 Z= 0.450 Chirality : 0.055 0.311 1307 Planarity : 0.006 0.059 1526 Dihedral : 13.126 166.343 3342 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.34 % Allowed : 4.35 % Favored : 95.31 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP H 700 HIS 0.007 0.001 HIS H 640 PHE 0.027 0.003 PHE E 142 TYR 0.016 0.002 TYR H 648 ARG 0.006 0.001 ARG H 96 *********************** 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 : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 42 TRP cc_start: 0.8712 (t60) cc_final: 0.8495 (t60) REVERT: E 137 LYS cc_start: 0.8340 (mptt) cc_final: 0.7996 (mmmm) REVERT: E 151 LYS cc_start: 0.8601 (tttm) cc_final: 0.8361 (ttmm) REVERT: F 69 TRP cc_start: 0.6550 (m-10) cc_final: 0.6336 (m-10) REVERT: H 144 LYS cc_start: 0.8006 (tmmt) cc_final: 0.7708 (tttt) REVERT: H 146 MET cc_start: 0.6523 (tpp) cc_final: 0.6291 (mtt) REVERT: H 326 TYR cc_start: 0.6030 (t80) cc_final: 0.5239 (m-80) REVERT: H 346 LEU cc_start: 0.8714 (mt) cc_final: 0.8457 (mt) REVERT: H 450 GLN cc_start: 0.8231 (mt0) cc_final: 0.7745 (mm110) REVERT: H 639 LYS cc_start: 0.8393 (tptp) cc_final: 0.8187 (tttm) outliers start: 3 outliers final: 0 residues processed: 237 average time/residue: 0.2778 time to fit residues: 83.6532 Evaluate side-chains 136 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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: 0.9980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 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: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.8123 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9057 Z= 0.242 Angle : 0.588 10.857 12323 Z= 0.308 Chirality : 0.044 0.194 1307 Planarity : 0.005 0.053 1526 Dihedral : 12.646 173.032 1359 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.29 % Allowed : 11.56 % Favored : 86.16 % 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: -3.55 (0.23), residues: 1049 helix: -1.92 (0.23), residues: 423 sheet: -2.46 (0.40), residues: 153 loop : -2.65 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 147 HIS 0.003 0.001 HIS F 145 PHE 0.019 0.002 PHE H 528 TYR 0.015 0.001 TYR F 193 ARG 0.007 0.001 ARG F 248 *********************** 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 173 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 1.011 Fit side-chains REVERT: E 42 TRP cc_start: 0.8745 (t60) cc_final: 0.8476 (t60) REVERT: E 84 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7486 (mtp85) REVERT: E 93 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8577 (tptp) REVERT: E 137 LYS cc_start: 0.8333 (mptt) cc_final: 0.7984 (mmmm) REVERT: E 151 LYS cc_start: 0.8711 (tttm) cc_final: 0.8497 (ttmt) REVERT: E 252 GLU cc_start: 0.8790 (tp30) cc_final: 0.8342 (tp30) REVERT: F 205 MET cc_start: 0.8624 (tpp) cc_final: 0.7920 (ttp) REVERT: F 251 MET cc_start: 0.7838 (tpp) cc_final: 0.7361 (tpp) REVERT: H 101 ASN cc_start: 0.8851 (p0) cc_final: 0.8555 (p0) REVERT: H 144 LYS cc_start: 0.8016 (tmmt) cc_final: 0.7658 (tttt) REVERT: H 168 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.5847 (tmm) REVERT: H 326 TYR cc_start: 0.5856 (t80) cc_final: 0.5209 (m-80) REVERT: H 450 GLN cc_start: 0.8253 (mt0) cc_final: 0.7851 (mm-40) REVERT: H 474 ILE cc_start: 0.9226 (mt) cc_final: 0.9005 (mt) REVERT: H 639 LYS cc_start: 0.8378 (tptp) cc_final: 0.8173 (tttm) outliers start: 20 outliers final: 15 residues processed: 167 average time/residue: 0.2618 time to fit residues: 56.9545 Evaluate side-chains 141 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 327 THR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 384 ASP Chi-restraints excluded: chain H residue 443 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9057 Z= 0.379 Angle : 0.647 8.713 12323 Z= 0.342 Chirality : 0.047 0.167 1307 Planarity : 0.005 0.058 1526 Dihedral : 12.813 173.415 1359 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.00 % Allowed : 13.39 % Favored : 82.61 % 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: -3.23 (0.24), residues: 1049 helix: -1.57 (0.24), residues: 426 sheet: -2.29 (0.41), residues: 153 loop : -2.56 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 700 HIS 0.004 0.001 HIS H 432 PHE 0.016 0.002 PHE E 142 TYR 0.017 0.002 TYR H 648 ARG 0.007 0.001 ARG F 248 *********************** 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 165 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 130 time to evaluate : 1.008 Fit side-chains REVERT: E 42 TRP cc_start: 0.8885 (t60) cc_final: 0.8490 (t60) REVERT: E 93 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8649 (tptp) REVERT: E 128 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7141 (mmmt) REVERT: E 137 LYS cc_start: 0.8339 (mptt) cc_final: 0.7835 (mmmm) REVERT: E 151 LYS cc_start: 0.8745 (tttm) cc_final: 0.8486 (ttmt) REVERT: E 167 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: H 118 LYS cc_start: 0.8407 (mtpp) cc_final: 0.8142 (ttmm) REVERT: H 144 LYS cc_start: 0.8006 (tmmt) cc_final: 0.7637 (tttt) REVERT: H 168 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6254 (tmm) REVERT: H 326 TYR cc_start: 0.5915 (t80) cc_final: 0.5232 (m-80) REVERT: H 450 GLN cc_start: 0.8420 (mt0) cc_final: 0.7798 (mm-40) REVERT: H 474 ILE cc_start: 0.9280 (mt) cc_final: 0.9062 (mt) outliers start: 35 outliers final: 24 residues processed: 152 average time/residue: 0.2422 time to fit residues: 49.3519 Evaluate side-chains 148 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 327 THR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 384 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 519 ASP Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 0.0980 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 ** 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: 0.8160 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9057 Z= 0.206 Angle : 0.536 8.451 12323 Z= 0.282 Chirality : 0.043 0.176 1307 Planarity : 0.004 0.064 1526 Dihedral : 12.457 173.523 1359 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.00 % Allowed : 14.87 % Favored : 81.12 % 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: -2.67 (0.25), residues: 1049 helix: -1.08 (0.25), residues: 424 sheet: -2.04 (0.42), residues: 152 loop : -2.27 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 147 HIS 0.004 0.001 HIS F 145 PHE 0.013 0.001 PHE F 196 TYR 0.013 0.001 TYR F 193 ARG 0.007 0.000 ARG F 248 *********************** 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 169 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 1.028 Fit side-chains REVERT: E 137 LYS cc_start: 0.8293 (mptt) cc_final: 0.7767 (mmmm) REVERT: E 151 LYS cc_start: 0.8729 (tttm) cc_final: 0.8436 (ttmt) REVERT: E 167 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: F 251 MET cc_start: 0.8153 (tpp) cc_final: 0.7933 (tpp) REVERT: H 109 LEU cc_start: 0.8746 (tp) cc_final: 0.8366 (tp) REVERT: H 144 LYS cc_start: 0.7992 (tmmt) cc_final: 0.7611 (tttt) REVERT: H 168 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6106 (tmm) REVERT: H 326 TYR cc_start: 0.5947 (t80) cc_final: 0.5269 (m-80) REVERT: H 351 TRP cc_start: 0.7654 (t60) cc_final: 0.7437 (t60) REVERT: H 450 GLN cc_start: 0.8414 (mt0) cc_final: 0.7782 (mm-40) REVERT: H 474 ILE cc_start: 0.9274 (mt) cc_final: 0.9035 (mt) outliers start: 35 outliers final: 24 residues processed: 156 average time/residue: 0.2392 time to fit residues: 50.3675 Evaluate side-chains 150 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 327 THR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 384 ASP Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN 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: 0.8161 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9057 Z= 0.219 Angle : 0.550 10.509 12323 Z= 0.283 Chirality : 0.043 0.164 1307 Planarity : 0.004 0.065 1526 Dihedral : 12.312 173.312 1359 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.46 % Allowed : 15.33 % Favored : 80.21 % 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: -2.47 (0.25), residues: 1049 helix: -0.85 (0.25), residues: 426 sheet: -1.92 (0.44), residues: 143 loop : -2.25 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 97 HIS 0.003 0.001 HIS F 145 PHE 0.011 0.001 PHE H 528 TYR 0.012 0.001 TYR F 193 ARG 0.008 0.000 ARG F 248 *********************** 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 164 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 1.069 Fit side-chains REVERT: E 128 LYS cc_start: 0.7284 (mmmt) cc_final: 0.7072 (mmmt) REVERT: E 137 LYS cc_start: 0.8325 (mptt) cc_final: 0.7770 (mmmm) REVERT: E 151 LYS cc_start: 0.8692 (tttm) cc_final: 0.8387 (ttmt) REVERT: E 167 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: E 252 GLU cc_start: 0.8773 (tp30) cc_final: 0.8309 (tp30) REVERT: F 251 MET cc_start: 0.8263 (tpp) cc_final: 0.8035 (tpp) REVERT: H 109 LEU cc_start: 0.8675 (tp) cc_final: 0.8246 (tp) REVERT: H 144 LYS cc_start: 0.7983 (tmmt) cc_final: 0.7652 (tttt) REVERT: H 168 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6140 (tmm) REVERT: H 326 TYR cc_start: 0.6029 (t80) cc_final: 0.5299 (m-80) REVERT: H 450 GLN cc_start: 0.8413 (mt0) cc_final: 0.7765 (mm-40) REVERT: H 474 ILE cc_start: 0.9258 (mt) cc_final: 0.9019 (mt) outliers start: 39 outliers final: 28 residues processed: 149 average time/residue: 0.2418 time to fit residues: 48.5030 Evaluate side-chains 149 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 52 ARG Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 327 THR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 384 ASP Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 498 HIS Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.0770 chunk 20 optimal weight: 0.4980 chunk 60 optimal weight: 0.0050 chunk 25 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.2330 ------------------------------------------------------------------------------- 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: 0.8068 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9057 Z= 0.131 Angle : 0.498 8.386 12323 Z= 0.255 Chirality : 0.041 0.160 1307 Planarity : 0.004 0.066 1526 Dihedral : 12.117 175.013 1359 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.20 % Allowed : 17.73 % Favored : 79.06 % 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: -1.96 (0.26), residues: 1049 helix: -0.31 (0.27), residues: 412 sheet: -1.67 (0.41), residues: 165 loop : -2.02 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 351 HIS 0.003 0.000 HIS F 145 PHE 0.011 0.001 PHE H 528 TYR 0.011 0.001 TYR H 154 ARG 0.007 0.000 ARG F 248 *********************** 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 166 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 0.918 Fit side-chains REVERT: E 128 LYS cc_start: 0.7191 (mmmt) cc_final: 0.6897 (mmmt) REVERT: E 137 LYS cc_start: 0.8261 (mptt) cc_final: 0.7730 (mmmm) REVERT: E 151 LYS cc_start: 0.8654 (tttm) cc_final: 0.8334 (ttmt) REVERT: F 251 MET cc_start: 0.8313 (tpp) cc_final: 0.8106 (tpp) REVERT: H 109 LEU cc_start: 0.8673 (tp) cc_final: 0.8282 (tp) REVERT: H 144 LYS cc_start: 0.8002 (tmmt) cc_final: 0.7640 (tttt) REVERT: H 168 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.5955 (tmm) REVERT: H 326 TYR cc_start: 0.5957 (t80) cc_final: 0.5236 (m-80) REVERT: H 450 GLN cc_start: 0.8360 (mt0) cc_final: 0.7751 (mm-40) outliers start: 28 outliers final: 20 residues processed: 157 average time/residue: 0.2319 time to fit residues: 48.8097 Evaluate side-chains 139 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 384 ASP Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 498 HIS Chi-restraints excluded: chain H residue 519 ASP Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 61 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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: 0.8126 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9057 Z= 0.201 Angle : 0.541 10.164 12323 Z= 0.275 Chirality : 0.043 0.158 1307 Planarity : 0.004 0.064 1526 Dihedral : 12.149 179.870 1359 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.66 % Allowed : 18.54 % Favored : 77.80 % 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: -1.83 (0.26), residues: 1049 helix: -0.20 (0.27), residues: 419 sheet: -1.65 (0.42), residues: 155 loop : -1.95 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 147 HIS 0.002 0.001 HIS F 145 PHE 0.008 0.001 PHE H 58 TYR 0.010 0.001 TYR F 193 ARG 0.007 0.000 ARG F 248 *********************** 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 154 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 0.900 Fit side-chains REVERT: E 137 LYS cc_start: 0.8274 (mptt) cc_final: 0.7731 (mmmm) REVERT: E 151 LYS cc_start: 0.8655 (tttm) cc_final: 0.8351 (ttmt) REVERT: H 109 LEU cc_start: 0.8647 (tp) cc_final: 0.8284 (tp) REVERT: H 144 LYS cc_start: 0.7993 (tmmt) cc_final: 0.7633 (tttt) REVERT: H 168 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6017 (tmm) REVERT: H 326 TYR cc_start: 0.5991 (t80) cc_final: 0.5263 (m-80) REVERT: H 450 GLN cc_start: 0.8397 (mt0) cc_final: 0.7800 (mm-40) REVERT: H 624 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8438 (tt) outliers start: 32 outliers final: 26 residues processed: 146 average time/residue: 0.2347 time to fit residues: 46.1286 Evaluate side-chains 146 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 498 HIS Chi-restraints excluded: chain H residue 519 ASP Chi-restraints excluded: chain H residue 624 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 64 optimal weight: 0.0270 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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: 0.8122 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9057 Z= 0.191 Angle : 0.546 10.674 12323 Z= 0.274 Chirality : 0.042 0.151 1307 Planarity : 0.004 0.063 1526 Dihedral : 12.066 177.990 1359 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.20 % Allowed : 18.54 % Favored : 78.26 % 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: -1.68 (0.26), residues: 1049 helix: -0.04 (0.27), residues: 414 sheet: -1.67 (0.43), residues: 150 loop : -1.86 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 147 HIS 0.004 0.001 HIS F 145 PHE 0.008 0.001 PHE H 528 TYR 0.010 0.001 TYR F 193 ARG 0.006 0.000 ARG H 52 *********************** 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 146 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.071 Fit side-chains REVERT: E 128 LYS cc_start: 0.7328 (mmmt) cc_final: 0.6996 (mmmt) REVERT: E 137 LYS cc_start: 0.8216 (mptt) cc_final: 0.7720 (mmmm) REVERT: E 151 LYS cc_start: 0.8652 (tttm) cc_final: 0.8350 (ttmt) REVERT: H 144 LYS cc_start: 0.7986 (tmmt) cc_final: 0.7631 (tttt) REVERT: H 168 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.5995 (tmm) REVERT: H 326 TYR cc_start: 0.5961 (t80) cc_final: 0.5278 (m-80) REVERT: H 351 TRP cc_start: 0.7763 (t60) cc_final: 0.7548 (t60) REVERT: H 450 GLN cc_start: 0.8402 (mt0) cc_final: 0.7798 (mm-40) REVERT: H 624 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8458 (tt) outliers start: 28 outliers final: 25 residues processed: 140 average time/residue: 0.2388 time to fit residues: 45.0472 Evaluate side-chains 139 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 327 THR Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 519 ASP Chi-restraints excluded: chain H residue 624 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.2980 chunk 97 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 0.0470 chunk 86 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 overall best weight: 0.3276 ------------------------------------------------------------------------------- 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: 0.8082 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9057 Z= 0.150 Angle : 0.518 9.437 12323 Z= 0.262 Chirality : 0.041 0.151 1307 Planarity : 0.003 0.061 1526 Dihedral : 11.939 177.756 1359 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.20 % Allowed : 19.22 % Favored : 77.57 % 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: -1.47 (0.26), residues: 1049 helix: 0.16 (0.27), residues: 413 sheet: -1.50 (0.41), residues: 166 loop : -1.77 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 147 HIS 0.002 0.000 HIS H 62 PHE 0.010 0.001 PHE H 528 TYR 0.010 0.001 TYR H 154 ARG 0.004 0.000 ARG H 52 *********************** 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 146 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 0.973 Fit side-chains REVERT: E 128 LYS cc_start: 0.7244 (mmmt) cc_final: 0.6942 (mmmt) REVERT: E 137 LYS cc_start: 0.8221 (mptt) cc_final: 0.7691 (mmmm) REVERT: E 151 LYS cc_start: 0.8658 (tttm) cc_final: 0.8348 (ttmt) REVERT: H 144 LYS cc_start: 0.7966 (tmmt) cc_final: 0.7612 (tttt) REVERT: H 168 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.5917 (tmm) REVERT: H 326 TYR cc_start: 0.5907 (t80) cc_final: 0.5202 (m-80) REVERT: H 351 TRP cc_start: 0.7709 (t60) cc_final: 0.7457 (t60) REVERT: H 450 GLN cc_start: 0.8413 (mt0) cc_final: 0.7821 (mm-40) REVERT: H 624 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8415 (tt) outliers start: 28 outliers final: 21 residues processed: 140 average time/residue: 0.2275 time to fit residues: 43.2713 Evaluate side-chains 135 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 327 THR Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 624 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8151 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9057 Z= 0.240 Angle : 0.569 9.702 12323 Z= 0.289 Chirality : 0.043 0.154 1307 Planarity : 0.004 0.061 1526 Dihedral : 12.015 177.332 1359 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.20 % Allowed : 19.34 % Favored : 77.46 % 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: -1.62 (0.26), residues: 1049 helix: -0.02 (0.27), residues: 414 sheet: -1.57 (0.43), residues: 150 loop : -1.83 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 147 HIS 0.003 0.001 HIS H 59 PHE 0.009 0.001 PHE F 71 TYR 0.011 0.001 TYR F 193 ARG 0.004 0.000 ARG H 52 ********************** 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 141 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 0.997 Fit side-chains REVERT: E 128 LYS cc_start: 0.7372 (mmmt) cc_final: 0.7065 (mmmt) REVERT: E 137 LYS cc_start: 0.8242 (mptt) cc_final: 0.7709 (mmmm) REVERT: E 151 LYS cc_start: 0.8641 (tttm) cc_final: 0.8343 (ttmt) REVERT: E 171 CYS cc_start: 0.8516 (m) cc_final: 0.8231 (t) REVERT: E 252 GLU cc_start: 0.8735 (tp30) cc_final: 0.8456 (tp30) REVERT: H 109 LEU cc_start: 0.8587 (tp) cc_final: 0.8240 (tp) REVERT: H 144 LYS cc_start: 0.7968 (tmmt) cc_final: 0.7597 (tttt) REVERT: H 168 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6114 (tmm) REVERT: H 326 TYR cc_start: 0.5965 (t80) cc_final: 0.5252 (m-80) REVERT: H 351 TRP cc_start: 0.7794 (t60) cc_final: 0.7537 (t60) REVERT: H 450 GLN cc_start: 0.8416 (mt0) cc_final: 0.7803 (mm-40) REVERT: H 624 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8479 (tt) outliers start: 28 outliers final: 24 residues processed: 134 average time/residue: 0.2388 time to fit residues: 43.1214 Evaluate side-chains 138 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 198 GLN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain H residue 327 THR Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 359 LYS Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 413 ASP Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 624 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 0.0010 chunk 4 optimal weight: 0.0870 overall best weight: 0.2364 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.157431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141229 restraints weight = 12360.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.143416 restraints weight = 8090.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144881 restraints weight = 5982.274| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9057 Z= 0.139 Angle : 0.520 9.419 12323 Z= 0.262 Chirality : 0.041 0.162 1307 Planarity : 0.003 0.059 1526 Dihedral : 11.886 177.368 1359 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.63 % Allowed : 19.91 % Favored : 77.46 % 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: -1.34 (0.27), residues: 1049 helix: 0.19 (0.27), residues: 420 sheet: -1.39 (0.41), residues: 165 loop : -1.66 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 147 HIS 0.002 0.000 HIS H 62 PHE 0.010 0.001 PHE H 528 TYR 0.010 0.001 TYR H 154 ARG 0.004 0.000 ARG H 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2069.09 seconds wall clock time: 38 minutes 17.98 seconds (2297.98 seconds total)